1000Genomes
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0199
application sub category: topic_0622
application sub category: topic_0625
application sub category: topic 3325
application sub category: topic 3365
application sub category: topic 3473
citation: nature09534
citation: nature11632
citation: nature15393
citation: nature15394
citation: pmcid:PMC3042601
citation: pmcid:PMC3498066
citation: pmcid:PMC4617611
citation: pmcid:PMC4750478
citation: pubmed:20981092
citation: pubmed:23128226
citation: pubmed:26432245
citation: pubmed:26432246
description: The 1000 Genomes Project ran between 2008 and 2015, creating a deep catalogue of human genetic variation. The International Genome Sample Resource (IGSR) was set up to ensure the future usability and accessibility of this data.
feature list: operation_0306
feature list: operation 3196
feature list: operation 3202
feature list: operation 3431
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
primary contact: Auton A

1000Genomes assembly converter
type: SoftwareApplication
input: Nucleic acid features
  type: FormalParameter
  additional type: data 1276
  encoding format: format 2305
  encoding format: format 2306
  encoding format: format 3003
  encoding format: format 3007
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
author: Ensembl team
description: Map your data to the current assembly.
feature list: operation 2944
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
software help: tools.html
software help: terms-of-use
software version: 1
primary contact: Ensembl Genomes webteam

1000Genomes data slicer
type: SoftwareApplication
input: Sequence coordinates
  type: FormalParameter
  additional type: data 2012
  encoding format: format 2572
  encoding format: format 3016
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
author: Ensembl Genomes team
citation: nmeth.1974
citation: pmcid:PMC3340611
citation: pubmed:22543379
description: Get a subset of data from a BAM or VCF file.
feature list: operation 2121
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
software help: tools.html
software help: terms-of-use
software version: 1
primary contact: Ensembl Genomes webteam

1000Genomes ID history converter
type: SoftwareApplication
input: Ensembl ID
  type: FormalParameter
  additional type: data 2610
output: Ensembl ID
  type: FormalParameter
  additional type: data 2610
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3345
author: Ensembl team
citation: 9781118782392.ch27
description: Convert a set of Ensembl IDs from a previous release into their current equivalents.
feature list: operation 3282
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
software help: tools.html
software help: terms-of-use
software version: 1
primary contact: Ensembl Genomes webteam

1000Genomes Variation Pattern Finder
type: SoftwareApplication
input: Sequence variations
  type: FormalParameter
  additional type: data 3498
  encoding format: format 3016
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
author: Ensembl Genomes team
author: Resequencing Informatics
citation: https://doi.org/10.1186/1471-2164-11-293
citation: pmcid:PMC2894800
citation: pubmed:20459805
contributor: Resequencing Informatics
description: Identify variation patterns in a chromosomal region of interest for different individuals.
feature list: operation 3504
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
software help: tools.html
software help: terms-of-use
software version: 1
primary contact: Ensembl Genomes webteam

1000Genomes VCF2PED
type: SoftwareApplication
input: Sequence variations
  type: FormalParameter
  additional type: data 3498
  encoding format: format 3016
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0199
author: Ensembl Genomes team
author: Resequencing Informatics
contributor: Resequencing Informatics
description: Convert a VCF file into a linkage pedigree file (ped) and a marker information file, which together may be loaded into ld visualization tools like Haploview.
feature list: operation_0335
provider: EMBL-EBI
software help: tools.html
software help: terms-of-use
software version: 1
primary contact: Ensembl Genomes webteam

123FASTQ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0769
application sub category: topic 3168
citation: https://doi.org/10.1101/2024.03.08.584032
description: 123FASTQ is a user-friendly software solution for preprocessing Illumina FASTQ reads, integrating quality control analysis, trimming, and format conversion. It aims to simplify NGS data preprocessing and improve workflow efficiency.
feature list: operation_0335
feature list: operation_0337
feature list: operation 3192
feature list: operation 3219
license: MIT

123VCF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0622
application sub category: topic 3577
application sub category: topic 3676
citation: s12859-024-05661-5
citation: pmcid:PMC10865685
citation: pubmed:38350858
description: An intuitive and efficient tool for filtering VCF files.
feature list: operation 3227
feature list: operation 3675
feature list: operation 3695
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

13Check_RNA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0099
application sub category: topic_0593
application sub category: topic_0749
citation: bty470
description: Tool to evaluate 13C chemical shift assignments of RNA.
feature list: operation 3431
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: A. A. Icazatti
primary contact: J. A. Vila

14-3-3-Pred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3534
citation: btv133
citation: pmcid:PMC4495292
citation: pubmed:25735772
description: Webserver that predicts 14-3-3-binding sites by combining predictions from three different classifiers: ANN, PSSM and SVM.
feature list: operation 2479
feature list: operation 2575
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
primary contact: The Barton Group

16S-ITGDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0637
application sub category: topic_0659
application sub category: topic 2229
application sub category: topic 3168
application sub category: topic 3174
citation: fbinf.2022.905489
citation: pmcid:PMC9580931
citation: pubmed:36304264
description: 16S-ITGDB is an integrated database for improving taxonomic classification of 16S ribosomal RNA (rRNA) sequences.
feature list: operation_0310
feature list: operation 3192
feature list: operation 3460
license: CC-BY-NC-SA-4.0

16S classifier
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0080
application sub category: topic_0659
application sub category: topic 3474
citation: journal.pone.0116106
citation: pmcid:PMC4315456
citation: pubmed:25646627
description: Random Forest based tool which is developed to carry out fast, efficient and accurate taxonomic classification of 16S rRNA sequences. It has the unique ability to classify small Hypervariable Regions of 16S rRNA.
feature list: operation 3460
operating system: Linux
software help: algorithm.html
primary contact: MetaBioSys Group

16SMicrobiomeMLFS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3474
description: Code and supporting data for the article: "Exploring the role of normalization and feature selection in microbiome disease classification pipelines."
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0009-0006-6618-7949

16sPIP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0080
application sub category: topic 3301
citation: s12859-017-1975-3
citation: pmcid:PMC5751400
citation: pubmed:29297318
description: Comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing.
feature list: operation 2454
operating system: Linux
software help: Manual-16sPIP.pdf
primary contact: Wen Zhang

1928 Diagnostics
type: SoftwareApplication
input: Nucleic acid features
  type: FormalParameter
  additional type: data 1276
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0091
application sub category: topic 2885
application sub category: topic 3673
description: Cloud-based platform. Providing bioinformatic analysis of bacteria. Species identification (16S, WGS), typing (MLST, cgMLST, SNP), antibiotic resistance profiling, virulence. Possibility to add metadata for transmission analysis.
feature list: operation 3840
operating system: Linux
operating system: Mac
operating system: Windows
software help: product

19andMe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic_0634
application sub category: topic 3305
citation: V1
description: 19 and Me: COVID-19 Risk Score Calculator is a tool that synthesizes reported COVID-19 geographic case data and rapidly evolving scientific research to help you ballpark how much risk this disease poses to you.
feature list: operation 2428
feature list: operation 3283
feature list: operation 3503
license: MIT
software help: 19andMe-APIdocumentation
primary contact: https://orcid.org/0000-0002-4299-3931

Geometrical interpretation of the 1-D DFT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3344
application sub category: topic 3382
description: Demonstrates Professor Grigoryan's illustration of geometrical interpretation of the 1-D DFT.
feature list: operation_0337
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.1.0.0
primary contact: Michael Chan

2-kupl
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic_0622
application sub category: topic 3168
citation: S12859-021-04185-6
citation: pmcid:PMC8180056
citation: pubmed:34090332
description: Mapping-free variant detection from DNA-seq data of matched samples.
feature list: operation_0524
feature list: operation 3192
feature list: operation 3227
feature list: operation 3436
feature list: operation 3472
is accessible for free: true
license: MIT

2019nCoVAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0622
application sub category: topic 3324
application sub category: topic 3673
citation: tcbb.2021.3049617
citation: pmcid:PMC8769043
citation: pubmed:33406042
description: 2019nCoVAS is a web service for different analyses including transmission, genome, and psychological stress.
feature list: operation_0324
feature list: operation 2403
feature list: operation 2426

2020plus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0622
application sub category: topic 2640
application sub category: topic 3175
application sub category: topic 3474
citation: pnas.1616440113
citation: pmcid:PMC5167163
citation: pubmed:27911828
description: 2020plus classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene from small somatic variants by using Random Forests.
feature list: operation_0276
feature list: operation_0313
feature list: operation 2454
feature list: operation 3197
feature list: operation 3225
feature list: operation 3504
is accessible for free: true
license: Apache-2.0
operating system: Linux
software help: index.html#
software version: v1.2.2
primary contact: https://orcid.org/0000-0003-1395-5378

2DProts
type: SoftwareApplication
input: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1475
output: Protein structure image
  type: FormalParameter
  additional type: data 2992
  encoding format: format 3547
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
application sub category: topic 1317
description: A database including visualizations of protein secondary structure via 2D diagrams. The 2D diagrams are based on whole protein family and they take into account 2D structure of the protein family members.
feature list: operation 2486
is accessible for free: true
license: Freeware
operating system: Linux
operating system: Mac
operating system: Windows

2StrucCompare
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0166
application sub category: topic_0736
application sub category: topic 3542
citation: GKZ456
citation: pmcid:PMC6602421
citation: pubmed:31114904
description: Webserver for the comparison of secondary structure algorithms and the secondary structure of protein structures.
feature list: operation_0267
feature list: operation_0319
feature list: operation 2488
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
primary contact: Elliot Drew
primary contact: Robert W. Janes

2B-Alert Web
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2815
application sub category: topic 3318
application sub category: topic 3520
citation: https://doi.org/10.2196/29595
citation: sleep.6318
citation: pmcid:PMC5103804
citation: pmcid:PMC8832274
citation: pubmed:27634801
citation: pubmed:35084336
description: 2B-Alert Web, an open-access tool for predicting neurobehavioral performance, which accounts for the effects of sleep/wake schedules, time of day, and caffeine consumption, while incorporating the latest scientific findings in sleep restriction, sleep extension, and recovery sleep.
feature list: operation 2426
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

coex-simulation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0204
application sub category: topic_0749
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/2024.10.24.619521
description: coex-simulation is a computational simulator developed to explore the relationship between events in single cells and bulk tissue expression profiles, aiming to clarify conditions under which intracellular regulatory signals propagate. The simulator and related data are available on Borealis and GitHub.
feature list: operation 3436
feature list: operation 3463

2D Image cepstral analysis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3344
application sub category: topic 3382
application sub category: topic 3474
description: Two dimensional cepstral spectrum. The present function calculates the cepstral spectrum of image either gray scale or RGB colored. This spectrum is useful for analysis of an image and suitable for pre-processing of an image for machine learning purposes.
feature list: operation 3443
feature list: operation 3860
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: Pavel Paunov

2D-MH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0154
citation: j.jtbi.2010.08.007
citation: pubmed:20696175
description: Web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids.
feature list: operation_0337
feature list: operation 2479
operating system: Linux
operating system: Mac
operating system: Windows
software help: 2D-MH
primary contact: Xiao Lab
primary contact: Xuan Xiao

2D-PAGE
type: SoftwareApplication
input: Spot ID
  type: FormalParameter
  additional type: data 2373
input: Protein isoelectric point
  type: FormalParameter
  additional type: data 1528
input: Peptide molecular weights
  type: FormalParameter
  additional type: data 1519
input: UniProt accession
  type: FormalParameter
  additional type: data 3021
input: Accession
  type: FormalParameter
  additional type: data 2091
output: 2D PAGE image
  type: FormalParameter
  additional type: data_0942
output: Protein property
  type: FormalParameter
  additional type: data_0897
  encoding format: format 2331
output: Protein isoelectric point
  type: FormalParameter
  additional type: data 1528
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0121
citation: pmic.200300483
citation: pubmed:12923769
description: 2D-PAGE database.
feature list: operation_0224
operating system: Linux
operating system: Mac
operating system: Windows
provider: University of Siena, Italy
software help: 2d.cgi
primary contact: Luca Bini

2dSS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0082
application sub category: topic_0623
application sub category: topic 3542
citation: https://doi.org/10.1101/649426
description: Web server for protein secondary structure visualization.
feature list: operation_0468
feature list: operation_0470
feature list: operation_0570
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: support.html
primary contact: Juliana S.. Bernardes

2D Digital Mammography Harmonization (EUCAIM-SW-046_T-01-03-008)
type: SoftwareApplication
input: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3548
input: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 3464
input: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3548
output: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3548
output: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3548
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0219
application sub category: topic 3071
application sub category: topic 3316
application sub category: topic 3382
author: Manuel Marfil-Trujillo
description: This preprocessing tool is design for 2D digital mammograms in DICOM format. It standardizes and harmonizes images through a configurable pipeline that includes spatial reorientation, pseudo-3D stacking, isotropic resampling, intensity normalization, optional denoising, contrast enhancement, and mask processing (if available).
feature list: operation 3695
is accessible for free: true
license: CC-BY-NC-ND-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://drive.google.com/file/d/1UK5qjmd0eHmMByYO1zC-2pRdP4gAmc0l/view
software help: https://drive.google.com/file/d/1tlpW4J3ZWtyfY-4gy3_TvkEb9CtUtOf8/view
software version: 1.1.0
primary contact: https://orcid.org/0000-0002-9506-9451

2D AR and 2D ARMA parameters estimation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
description: Algorithms for 2D AR and 2D ARMA parameters estimation.
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: Simona Maggio

2DE-pattern
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0078
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic 3520
citation: ELPS.201900468
citation: pubmed:32307725
description: 2DE-pattern is a database containing data on proteins/isoforms/proteoforms profiles.
feature list: operation 2421

2DImpute
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic_0622
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3676
citation: BTAA148
citation: pmcid:PMC7267828
citation: pubmed:32108864
description: An imputation method that recovers false zeros (known as dropouts) in single cell RNA sequencing (scRNA-seq) data. It features preventing excessive correction by predicting false zeros and imputing their values accurately by making use of the interrelationships between both genes and cells. 2DImpute takes as input a normalized scRNA-seq data matrix (genes in rows and cells in columns) with or without log-transformation. It outputs the imputed data in the same dimension and the same log-transformation.
feature list: operation 3435
feature list: operation 3557
license: GPL-3.0

2DKD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0108
application sub category: topic_0634
application sub category: topic 3382
citation: S13029-020-0077-1
citation: pmcid:PMC7011505
citation: pubmed:32064000
description: A toolkit for content-based local image search.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3443
license: GPL-3.0

2DSdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0611
application sub category: topic 3314
application sub category: topic 3318
citation: acs.jpclett.2c02972
citation: pubmed:36480578
description: The 2D semiconductor database (2DSdb) provides an ideal platform for computational modeling and design of new 2D semiconductors and heterostructures in photocatalysis, nanoscale devices, and other applications.
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows

2DX
type: SoftwareApplication
input: Raw image
  type: FormalParameter
  additional type: data 3424
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0611
application sub category: topic 1317
citation: j.jsb.2006.07.020
citation: pubmed:17055742
description: A software system designed as a user friendly, platform-independent software package for electron crystallography.
feature list: operation 3443
is accessible for free: true
operating system: Linux
operating system: Mac
provider: Instruct
software help: www.2dx.unibas.ch
software version: 1

2kplus2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2885
application sub category: topic 3053
citation: btu706
citation: pmcid:PMC4341063
citation: pubmed:25344498
description: Algorithm that searches graphs produced from the de novo assembler cortex.
feature list: operation_0484
feature list: operation 2421
feature list: operation 3225
operating system: Linux
software help: 2kplus2
primary contact: Team MacLean

2lpiRNApred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic_0798
application sub category: topic 3512
citation: https://doi.org/10.1080/15476286.2020.1734382
citation: pmcid:PMC7549647
citation: pubmed:32138598
description: 2lpiRNApred is a 2-layer integrated program for identifying piRNAs in the first layer and determining if piRNAs have the function of instructing target mRNA deadenylation in the second layer.
feature list: operation 3936
feature list: operation 3937

2passtools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3320
application sub category: topic 3512
citation: https://doi.org/10.1101/2020.05.27.118679
description: Two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing.
feature list: operation_0232
feature list: operation_0335
feature list: operation 3198
feature list: operation 3258
feature list: operation 3695
license: MIT

2SigFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0622
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 2269
application sub category: topic 3299
citation: S12859-020-3501-2
citation: pmcid:PMC7191778
citation: pubmed:32349677
description: 2SigFinder implements multiscale statistical algorithm to predict genomic islands from a single genome. It uses small-scale test with large-scale features to score small region deviating from the host and large-scale statistical test with small-scale features to identify multi-window segments for identification of genomic islands. 2SigFinder is a novel prediction method, the first combined use of small-scale and large-scale statistical testing for genomic island detection. 2SigFinder was tested by genomic island boundary detection and identification of genomic islands or functional features of real biological data. Genomic island (GI) is a cluster of genes in prokaryotic genomes that have probable horizontal origins.
feature list: operation_0362
feature list: operation_0430
feature list: operation 3461

3CDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 3176
citation: 978-1-60327-414-2 12
citation: pubmed:19588093
description: Manually curated 3C (Chromosome conformation capture) database.
feature list: operation_0224
is accessible for free: true
software help: FAQ.jsp

3D-ADA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3382
citation: BTZ364
citation: pmcid:PMC6612867
citation: pubmed:31510673
description: A method for adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms.
license: GPL-3.0

3D-Cardiomics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0204
application sub category: topic_0749
application sub category: topic 3300
application sub category: topic 3308
application sub category: topic 3335
citation: https://doi.org/10.1101/792002
description: 3D Cardiomics is a web application that enables the viewing of the 3D transcriptome of the human heart.
feature list: operation_0313
feature list: operation 2942
feature list: operation 3223

3DCNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0082
application sub category: topic 2814
application sub category: topic 3474
citation: JOURNAL.PONE.0221347
citation: pmcid:PMC6728020
citation: pubmed:31487288
description: A 3D convolutional neural network to estimate protein model accuarcy based on local structure quality assessment.
feature list: operation_0321
feature list: operation_0480
license: MIT

3DChrom
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0654
application sub category: topic_0659
application sub category: topic 3295
citation: S12859-019-3083-Z
citation: pmcid:PMC6886161
citation: pubmed:31787081
description: 3DChrom is a web application for reconstructing three-dimensional structures of chromatins and TADs using Hi-C data and multidimensional scaling.
feature list: operation_0320
feature list: operation 3432
feature list: operation 3435
software help: help.html

3D Genome Viewer (3DGV)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0122
application sub category: topic 3173
citation: https://doi.org/10.1101/855379
description: The 3D Genome Viewer is a deskop application to view and explore 3D genome models from Hi-C data using virtual reality technology. The goal of 3DGV is to build fully immersive VR genome browser where the user can seamlessly interact.
feature list: operation_0570
feature list: operation 3208
is accessible for free: true
operating system: Mac
operating system: Windows
software help: documentation
primary contact: https://orcid.org/0000-0002-2561-7117

3DMorph
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2229
application sub category: topic 3382
application sub category: topic 3421
citation: ENEURO.0266-18.2018
citation: pmcid:PMC6325541
citation: pubmed:30627639
description: Script that analyzes microglia morphology from 3D data. Outputs include cell and territorial volume, branch length, and number of branch and end points.
feature list: operation 3450
feature list: operation 3629
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

3DSlicer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0605
application sub category: topic 3315
application sub category: topic 3384
citation: PEERJ.PREPRINTS.27998V1
description: 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Related to bio.tools/fossilj.
feature list: operation 3443
software help: Main Page

3Dscript
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0176
application sub category: topic 3382
citation: s41592-019-0359-1
citation: pubmed:30886414
description: Creates high-quality 3D/4D animations using a natural-language based syntax.
feature list: operation_0250
feature list: operation_0337
is accessible for free: true
license: BSD-2-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: 3Dscript
primary contact: Benjamin Schmid

3SRP
type: SoftwareApplication
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1931
output: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3751
output: Clustered expression profiles
  type: FormalParameter
  additional type: data 3768
  encoding format: format 3508
  encoding format: format 3603
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic 3308
author: https://orcid.org/0000-0002-8571-7603
author: https://orcid.org/0000-0003-3237-7382
author: Dimitri MEISTERMANN
author: Philippe Bordron
citation: j.celrep.2020.108419
citation: j.jaut.2017.10.005
citation: s41419-020-2505-1
citation: s41467-017-02107-w
citation: s41598-017-14892-x
citation: jci.insight.90088
citation: v1
citation: fimmu.2017.02014
citation: ijms21041368
citation: nu12051464
citation: pmcid:PMC5291739
citation: pmcid:PMC5676863
citation: pmcid:PMC5783949
citation: pmcid:PMC5797797
citation: pmcid:PMC7072876
citation: pmcid:PMC7200824
citation: pmcid:PMC7284977
citation: pubmed:28194440
citation: pubmed:29054368
citation: pubmed:29116112
citation: pubmed:29367672
citation: pubmed:29445370
citation: pubmed:32085612
citation: pubmed:32371863
citation: pubmed:32438566
citation: pubmed:33238118
contributor: https://orcid.org/0000-0002-8689-2083
description: A Snakemake-based pipeline for 3' sequencing RNA profiling data analysis. This 3’ Digital gene expression sequencing technique allows a precise and low-cost transcriptome profiling. The main steps of the pipeline are: - Samples demultiplexing transform the raw paired-end fastq files into a single-end fastq file for each sample. - Alignment on refseq reference transcriptome is performed using bwa. - Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix. If secondary analysis has been asked (providing a comparisons file), the expression matrix is normalized and differentially expressed genes (DEG) are searched using deseq2. - If DEG are found, annotation is performed using the database GO and KEGG. - A report is provided listing the main quality controls performed and the results found. Cite : https://dx.doi.org/10.21203/rs.3.pex-1336/v1
feature list: operation_0531
feature list: operation 2935
feature list: operation 3223
feature list: operation 3563
is accessible for free: true
operating system: Linux
provider: BiRD bioinformatics facility
software help: home
software version: 1.0
primary contact: https://orcid.org/0000-0002-8571-7603

3 aQTL-atlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3517
citation: gkab740
citation: pmcid:PMC8728222
citation: pubmed:34432052
description: An atlas of 3'UTR alternative polyadenylation quantitative trait loci across human normal tissues.
feature list: operation 2943
feature list: operation 3196
feature list: operation 3208
feature list: operation 3232
feature list: operation 3799
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

3CAC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0798
application sub category: topic 3174
application sub category: topic 3697
citation: https://doi.org/10.1101/2021.11.05.467408
description: 3CAC is a three-class classifier designed to classify contigs in mixed metagenome assemblies as phages, plasmids, chromosomes, or uncertain. 3CAC generates its initial classification by existing classifiers: viralVerify, PPR-Meta, PlasClass, and deepVirFinder. Thus, prior to running 3CAC, installation of these tools are required.
feature list: operation_0310
feature list: operation 3472
feature list: operation 3731
is accessible for free: true
license: MIT
primary contact: https://orcid.org/0000-0003-1889-9870

3Cnet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0102
application sub category: topic_0634
application sub category: topic 3168
application sub category: topic 3474
citation: btab529
citation: pmcid:PMC8665754
citation: pubmed:34270679
description: Pathogenicity prediction of human variants using multitask learning with evolutionary constraints.
feature list: operation_0331
feature list: operation 3227
feature list: operation 3461
is accessible for free: true
license: CC-BY-NC-4.0
operating system: Linux
operating system: Mac
operating system: Windows

3d-SPADE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3300
application sub category: topic 3304
citation: J.BIOSYSTEMS.2019.104022
citation: pubmed:31449837
description: 3d-SPADE is a method to find reoccurring spike patterns in parallel spike train data, and to determine their statistical significance. It is a part of Elephant.
feature list: operation 3501
is accessible for free: true
license: BSD-3-Clause

3D-Beacons
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web API
additional type: Web service
application sub category: topic 1317
application sub category: topic 2275
citation: https://doi.org/10.1101/2022.08.01.501973
description: The 3D-Beacons Network provides unified programmatic access to experimentally determined and predicted structure models.
is accessible for free: true
license: Apache-2.0
software help: api
software help: docs
software help: guidelines
software version: 1.0.0
primary contact: https://orcid.org/0000-0002-3687-0839

3D-BioInfo + BioExcel: Protein Conformational Ensembles Generation
type: SoftwareApplication
input: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1476
output: Trajectory data
  type: FormalParameter
  additional type: data 3870
  encoding format: format 1476
  encoding format: format 3464
  encoding format: format 3874
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0081
application sub category: topic_0082
application sub category: topic_0092
application sub category: topic 3510
application sub category: topic 3892
author: Adam Hospital
citation: s41597-019-0177-4
citation: f1000research.20559.1
citation: pmcid:PMC6736963
citation: pmcid:PMC7284151
citation: pubmed:31506435
citation: pubmed:32566135
contributor: Genís Bayarri
description: This workflow illustrates the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb). Workflow included in the ELIXIR 3D-Bioinfo Implementation Study: Building on PDBe-KB to chart and characterize the conformation landscape of native proteins
feature list: operation_0250
feature list: operation_0474
feature list: operation 2406
feature list: operation 2939
feature list: operation 3890
feature list: operation 3891
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: 3D-BioInfo
software help: https://biobb-wf-flexdyn.readthedocs.io/en/latest/
software version: 1.0
primary contact: Adam Hospital

3D-BLAST beta
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0078
application sub category: topic 2814
citation: gb-2007-8-3-r31
citation: pmcid:PMC1868941
citation: pubmed:17335583
description: 3D-BLAST is a very fast and accurate method for discovering the homologous proteins and evolutionary classifications of a newly determined protein structure.
feature list: operation 2421
feature list: operation 2479
operating system: Linux
operating system: Mac
operating system: Windows
software help: intro.php
software version: 1.02

3D-Cell-Annotator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic 2229
application sub category: topic 3383
application sub category: topic 3384
citation: BTAA029
citation: pmcid:PMC7203751
citation: pubmed:31950986
description: An open-source active surface tool for single-cell segmentation in 3D microscopy images. It is a plugin for Medical Imaging Interaction Toolkit (https://www.mitk.org/).
feature list: operation 3552

3D CT MRI images interactive sliding viewer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3306
application sub category: topic 3344
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3452
description: An interactive tool for users to browse through sagittal, axial and coronal views of CT/MRI images.
feature list: operation 3443
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.3.0.0
primary contact: Gang Wang

3D-DART
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0092
application sub category: topic_0097
application sub category: topic_0593
application sub category: topic 1317
author: http://orcid.org/0000-0001-7369-1322
citation: gkp287
citation: pmcid:PMC2703913
citation: pubmed:19417072
description: A web server for generation of 3D-structural DNA models with a defined conformation by providing control over both ‘global’ and ‘local’ conformational features.
feature list: operation_0570
feature list: operation 2476
feature list: operation 2481
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
provider: http://orcid.org/0000-0001-7369-1322
software help: DARTusage.html
software version: 1
primary contact: http://orcid.org/0000-0001-7369-1322

3D Diffusion gradient
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3315
application sub category: topic 3344
application sub category: topic 3382
description: Generate in 3D the diffusion gradient vector field as in Xu and Prince 1998
feature list: operation 3443
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.2.0.0
primary contact: Khaled Khairy

3d-dna
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0654
citation: science.aal3327
citation: pmcid:PMC5635820
citation: pubmed:28336562
description: 3D de novo assembly (3D-DNA) is a pipeline for de novo assembly using HiC.
feature list: operation_0524
feature list: operation_0525
feature list: operation 3216
license: MIT
primary contact: http://orcid.org/0000-0003-0634-6486

3D-e-Chem-VM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0081
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 2258
application sub category: topic 3314
citation: ACS.JCIM.6B00686
citation: pmcid:PMC5342320
citation: pubmed:28125221
description: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.
feature list: operation 2406
feature list: operation 2414
feature list: operation 3646
operating system: Linux
operating system: Mac
operating system: Windows
software help: wiki
primary contact: C. De. Graaf
primary contact: Ross Mcguire
primary contact: S. Verhoeven

3D-Footprint
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0078
application sub category: topic_0081
application sub category: topic_0157
application sub category: topic 3534
citation: gkp781
citation: pmcid:PMC2808867
citation: pubmed:19767616
description: 3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Comparisons with expert-curated databases RegulonDB and TRANSFAC support the quality of structure-based estimates of specificity.
feature list: operation_0321
feature list: operation_0478
feature list: operation 2997
feature list: operation 3561
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial.html
primary contact: 3D-Footprint Support

3D Free Form Image Registration Toolbox (GUI)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3306
application sub category: topic 3344
application sub category: topic 3382
description: A toolbox for performing image registrations on 4D RTOG files or any other volumetric image.
feature list: operation 3443
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.5.0.0
primary contact: Daniel Markel

3D-Fun
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0821
application sub category: topic 2275
application sub category: topic 2814
citation: gkn308
citation: pmcid:PMC2447717
citation: pubmed:18515349
description: Software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.
feature list: operation_0320
feature list: operation_0321
feature list: operation_0474
feature list: operation_0477
feature list: operation 2487

3D-GNOME
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0621
application sub category: topic 3175
application sub category: topic 3176
application sub category: topic 3940
citation: GKAA388
citation: pmcid:PMC7319547
citation: pubmed:32442297
description: 3D chromatin organization webserver is a 3D genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. 3D genome organization plays a critical role in its functioning. Alterations of this organization caused by structural variants (SVs) may lead to changes in gene transcription or even to disease. The recent advent of Chromosome Conformation Capture (3C) based techniques such as ChIA-PET and Hi-C allows us to investigate genome spatial organization. The rising volume of sequencing data in turn enables highly accurate identification of structural variation. Combination of those two sources of information can reveal mechanisms of genome regulation.
feature list: operation_0481
feature list: operation_0570
feature list: operation 3196
software version: 2.0

3D image stacker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3344
application sub category: topic 3382
description: MATLAB script for converting a image stack into a 3D array.
feature list: operation 3443
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: boyexex

3D-Jury
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0736
application sub category: topic 2814
application sub category: topic 3542
citation: btg124
citation: gkg503
citation: gkg504
citation: pmcid:PMC168910
citation: pmcid:PMC168911
citation: pubmed:12761065
citation: pubmed:12824309
citation: pubmed:12824423
description: 3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.
feature list: operation_0267
feature list: operation_0268
feature list: operation_0474
feature list: operation_0477

3D Kinematics and Inverse Dynamics
type: SoftwareApplication
input: Peptide hydrophobic moment
  type: FormalParameter
  additional type: data 1520
input: Protein sequence hydropathy plot
  type: FormalParameter
  additional type: data 1522
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
description: Computations of joint angles and displacements, moments and forces (lower / upper limb)
feature list: operation_0407
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 2.2
primary contact: Raphael Dumas

3D-partner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0128
application sub category: topic_0157
application sub category: topic_0602
citation: gkm346
citation: pmcid:PMC1933210
citation: pubmed:17517763
description: Tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.
feature list: operation_0474
feature list: operation 2406
feature list: operation 2479
feature list: operation 2492
feature list: operation 2575
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: intro.php
primary contact: Jinn-Moon Yang
primary contact: Yu-Shu Lo

3D PHOVIS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3383
application sub category: topic 3384
application sub category: topic 3452
application sub category: topic 3954
citation: j.pacs.2020.100168
citation: pmcid:PMC7082691
citation: pubmed:32211292
description: 3D photoacoustic visualization studio. Bio Optics and Acoustics Laboratory.
feature list: operation_0297
feature list: operation_0337
feature list: operation 3443

3D-pssm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0130
application sub category: topic_0160
application sub category: topic_0736
citation: pubmed:10526371
citation: pubmed:10860755
description: Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.
feature list: operation_0245
feature list: operation_0267
feature list: operation_0303
feature list: operation_0474
operating system: Linux
operating system: Mac
operating system: Windows
software help: index2.html
primary contact: Lawrence Kelley

3d-qsar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0209
application sub category: topic 2258
application sub category: topic 2275
application sub category: topic 3375
citation: S10822-019-00231-X
citation: pubmed:31595406
description: 3D-QSAR is a web portal that brings 3-D QSAR to all electronic devices-the Py-CoMFA web application as tool to build models from pre-aligned datasets. The underlying idea of any field-based 3-D QSAR is that differences in a target propriety, e.g., biological activity, are often closely related to equivalent changes in shapes and intensities of noncovalent calculated interaction surrounding the molecules (also called molecular interaction fields, MIFs).
feature list: operation_0478
feature list: operation 3435
feature list: operation 3659

3D RNA-seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3518
citation: https://doi.org/10.1080/15476286.2020.1858253
citation: pmcid:PMC8594885
citation: pubmed:33345702
description: 3D RNA-seq appA powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. 3D RNA-seq is currently under a dual-licensing model.
feature list: operation_0264
feature list: operation 2939
feature list: operation 3223
feature list: operation 3680
feature list: operation 3800

3D Shepp-Logan Phantom
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3344
application sub category: topic 3382
description: 3D Shepp-Logan Phantom is a 3D extension of MATLAB's phantom function - generates a phantom consisting of an arbitrary number of ellipsoids in 3D.
feature list: operation 3755
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: Patrick Bolan

3D Fluorescence Speckle Analyzer (3D-Speckler)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 2229
application sub category: topic 3382
citation: BIOPROTOC.5051
citation: pmcid:PMC11349494
citation: pubmed:39210955
description: 3D-Speckler is a semi-automated software tool for calibrating fluorescence microscopy, enabling precise quantification of fluorescence puncta, including nanoscale 2D/3D particle size, precise locations, and intensity information. It utilizes multispectral fluorescence beads of known sizes alongside the software to calibrate imaging systems.
feature list: operation 2238
feature list: operation 3457
feature list: operation 3799

3D-SURFER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0166
citation: 978-1-4939-0366-5 8
citation: pubmed:24573477
description: 3D-SURFER is a web-based tool for real-time protein surface comparison and analysis. The server integrates a repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons.
feature list: operation 2479
feature list: operation 3351
feature list: operation 3666
software help: tutorial.php

3D-XGuide
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3067
application sub category: topic 3444
application sub category: topic 3452
application sub category: topic 3954
citation: s11548-020-02274-0
citation: pmcid:PMC7822775
citation: pubmed:33057891
description: 3D-XGuide is a software framework providing a foundation for rapid prototyping of new approaches in the field of XR navigation guidance. Actual software release offers graphical user interface with basic functionality including data import and handling, calculation of projection geometry and transformations between related coordinate systems, rigid 3D-3D registration, and template-matching-based tracking and motion compensation algorithms in 2D and 3D.
feature list: operation_0337
feature list: operation 3443
license: BSD-2-Clause

3dRNA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0099
citation: IJMS20174116
citation: pmcid:PMC6747482
citation: pubmed:31450739
description: An Web Server for RNA 3D structure prediction.
feature list: operation_0278
feature list: operation_0502
feature list: operation 2441
software version: v2.0

3D Spine Analysis Software (3dSpAn)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3070
application sub category: topic 3382
citation: S12021-021-09549-0
citation: pubmed:34743262
description: An interactive software for 3D segmentation and analysis of dendritic spines.
feature list: operation 3450
feature list: operation 3799
software help: 3dSpAn supplementary.pdf
primary contact: 0000-0002-7269-983X
primary contact: https://orcid.org/0000-0003-1780-0461
primary contact: Ewa Baczynska
primary contact: Nirmal Das

Three Dimensional Analytical Magnetic Resonance Imaging Phantom in the Fourier Domain
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3344
application sub category: topic 3444
description: This software contains 2D and 3D Shepp-Logan phantoms in both the image and Fourier domains.
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.1.0.0
primary contact: Cheng Guan Koay

3DBIONOTES
type: SoftwareApplication
input: EMDB ID
  type: FormalParameter
  additional type: data 1146
input: UniProt accession
  type: FormalParameter
  additional type: data 3021
input: PDB ID
  type: FormalParameter
  additional type: data 1127
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0078
application sub category: topic_0219
application sub category: topic 3047
application sub category: topic 3366
author: https://orcid.org/0000-0002-0735-4317
author: Joan Segura
citation: j.jsb.2016.02.007
citation: btab397
citation: btx483
citation: btz118
description: Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB structures and Uniprot sequences where the protein annotations stored in Uniprot, Immune Epitope DB, Phospho Site Plus, BioMuta and dSysMap can be explored interactively at sequence and structural level.
feature list: operation_0564
feature list: operation_0570
feature list: operation 2422
funder: CORBEL
funder: CSIC
funder: Comunidad de Madrid
funder: EOSC-Life
funder: Instituto de Salud Carlos III
funder: Spanish Ministry of Science and Innovation
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: ELIXIR-ES
provider: INB
provider: cnb.csic.es
software help: help
software version: v3
primary contact: https://orcid.org/0000-0003-2621-6806

3DCellSeg
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
additional type: Workflow
application sub category: topic_0780
application sub category: topic 2229
application sub category: topic 3382
application sub category: topic 3474
application sub category: topic 3500
citation: S41598-021-04048-3
citation: pmcid:PMC8748745
citation: pubmed:35013443
description: A light and robust tool to do 3D cell instance segmentation for cell membrane images. It is useful when the cells clump together.
feature list: operation 3443
feature list: operation 3552
feature list: operation 3553
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

3DCOMB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2814
citation: btr432
citation: pmcid:PMC3167051
citation: pubmed:21791532
description: 3DCOMB is a software which can generate a multiple structure alignment (MSA) with not only as many conserved cores as possible, but also high-quality pairwise alignments.
feature list: operation_0295
feature list: operation_0504
operating system: Linux
software version: 1.06

3DeFDR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2229
application sub category: topic 2269
application sub category: topic 3169
application sub category: topic 3295
citation: S13059-020-02061-9
citation: pmcid:PMC7496221
citation: pubmed:32859248
description: 3DeFDR is a statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data. An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Computational tools for rigorous assessment of cell type-specific loops across multiple biological conditions are needed. We present 3DeFDR, a simple and effective statistical tool for classifying dynamic loops across biological conditions from Chromosome-Conformation-Capture-Carbon-Copy (5C) and Hi-C data. Our work provides a statistical framework and open-source coding libraries for sensitive detection of cell type-specific loops in high-resolution 5C and Hi-C data from multiple cellular conditions
feature list: operation_0481
feature list: operation 3222
feature list: operation 3435
license: MIT

3DEM Loupe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic_0611
application sub category: topic 3382
application sub category: topic 3385
citation: gkt385
citation: pmcid:PMC3692114
citation: pubmed:23671335
description: 3DEM Loupe is a web-server that allows normal mode analysis of any uploaded electron microscopy volume. Results can be explored in 3 dimensions through animations and movies.
feature list: operation_0321
feature list: operation 2406
feature list: operation 3457
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: 3DEM Loupe Team

3DEMBenchmark
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3569
citation: https://doi.org/10.1007/978-3-642-28062-7
description: Robust computational infrastructure capable of supporting the automatic and standardised benchmarking of image processing applications for cryoEM.
feature list: operation 2428
operating system: Linux
operating system: Mac
operating system: Windows
provider: cnb.csic.es
software help: LoadHelp.htm
primary contact: Joan Segura

3DFI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic_0082
application sub category: topic_0121
application sub category: topic_0769
application sub category: topic 2814
application sub category: topic 3400
citation: vbab030
citation: pmcid:PMC9162058
citation: pubmed:35664289
description: The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.
feature list: operation_0303
feature list: operation_0474
feature list: operation_0570
feature list: operation 3663
feature list: operation 3767
is accessible for free: true
license: MIT
operating system: Linux

3DGenBench
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic_0199
application sub category: topic_0621
application sub category: topic 3169
application sub category: topic 3912
citation: gkac396
citation: pmcid:PMC9252746
citation: pubmed:35639501
description: A web-server to benchmark computational models for 3D Genomics.
feature list: operation_0475
feature list: operation 2483
feature list: operation 3435
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

3DGene
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0114
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3295
application sub category: topic 3306
citation: J.XGEN.2024.100698
citation: pmcid:PMC11701261
citation: pubmed:39591973
description: 3DGene is a database and visualization tool that provides predicted 3D conformations of active genes in GM12878 human lymphoblastoid cells, generated using the e-HiP-HoP framework. The database offers interactive visualizations and downloadable simulation data, revealing insights into gene structure and regulatory networks.
feature list: operation_0337
feature list: operation 2454
feature list: operation 2476
feature list: operation 3216
feature list: operation 3927

3DGT-DDI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic 3336
application sub category: topic 3375
application sub category: topic 3474
citation: bbac134
citation: pubmed:35511112
description: 3D graph and text based neural network for drug-drug interaction prediction.
feature list: operation 3625
feature list: operation 3927
feature list: operation 4009
license: Apache-2.0

3DIANA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic_0128
application sub category: topic_0602
application sub category: topic 2275
author: Joan Segura
citation: j.bpj.2015.11.3519
citation: pmcid:PMC4775853
citation: pubmed:26772592
description: 3DIANA (3D Domain Interaction Analysis) is a web based environment designed to integrate bioinformatics-like information for the analysis of protein interactions and quaternary structure modellling
feature list: operation 2949
feature list: operation 3350
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html

3DID database of 3D interacting domains
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0128
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic_0736
citation: gkq962
citation: pmcid:PMC3013799
citation: pubmed:20965963
description: Collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The web server visualizes these interfaces along with atomic details of individual interactions using Jmol.
feature list: operation_0246
feature list: operation_0248
feature list: operation_0303
feature list: operation 2492
feature list: operation 2949
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
primary contact: Patrick Aloy

3DIV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0204
application sub category: topic_0621
application sub category: topic 2640
application sub category: topic 3295
citation: gkaa1078
citation: pmcid:PMC7778885
citation: pubmed:33245777
description: 3D-Genome Interaction Viewer & database is a comprehensive resource of 3D genome and 3D cancer genome. 3D genome organization is tightly coupled with gene regulation in various biological processes and diseases. 3D Interaction Viewer and Database (3DIV) is a database providing chromatin interaction visualization in a variety of options from one-to-all chromatin interaction with epigenetic annotation to unique dynamic browsing tools allowing examination of large-scale genomic rearrangement mediated impacts in cancer 3D genome.
feature list: operation 2429
feature list: operation 3208
feature list: operation 3435
is accessible for free: true
software help: tutorial

3DLigandSite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic_0154
application sub category: topic 2814
application sub category: topic 3511
application sub category: topic 3534
citation: gkq406
citation: pmcid:PMC2896164
citation: pubmed:20513649
description: 3DLigandSite is a web server for the prediction of ligand binding sites. Ligands bound to similar protein structures as the query structure are used to predict the binding site.
feature list: operation_0474
feature list: operation_0482
feature list: operation 2575
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Mark Wass

3dLOGO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0121
application sub category: topic_0166
citation: jmbi.1998.2248
citation: gkm228
citation: https://doi.org/10.1186/1471-2105-5-50
citation: 1471-2105-6-s4-s5
citation: pmcid:PMC1866380
citation: pmcid:PMC1933223
citation: pmcid:PMC420233
citation: pubmed:15119965
citation: pubmed:16351754
citation: pubmed:17488847
citation: pubmed:9837739
description: 3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.
feature list: operation_0245
feature list: operation_0448
feature list: operation 2406
feature list: operation 2479
feature list: operation 3767

3Dmapper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0622
application sub category: topic 2814
application sub category: topic 3120
application sub category: topic 3676
citation: btae171
citation: pmcid:PMC11018535
citation: pubmed:38565273
description: A command line tool for bio bank-scale mapping of variants to protein structures.
feature list: operation_0321
feature list: operation_0331
feature list: operation_0477
feature list: operation 2429
feature list: operation 3227
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

3DMem-enzyme
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Workbench
application sub category: topic_0821
application sub category: topic 3297
application sub category: topic 3306
application sub category: topic 3398
application sub category: topic 3569
citation: j.memsci.2016.11.013
description: This is an in-house code of the FORTH/ICE-HT Laboratory of Simulation of Advanced Materials and Processes, Patras, Greece, providing a reliable 3D reconstruction and simulation of a membrane bioreactor for lactose hydrolysis with immobilized enzymes. The membrane model is coupled to a macroscopic model of a single membrane fiber unit to produce lactose concentration profiles, lactose consumption predictions, and performance index estimates.
feature list: operation_0250
feature list: operation_0322
feature list: operation_0477
feature list: operation 2476
primary contact: Vassilios Burganos

3Dmol.js
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 3314
application sub category: topic 3382
citation: acs.jchemed.0c00579
citation: btu829
citation: pmcid:PMC4393526
citation: pmcid:PMC9416521
citation: pubmed:25505090
citation: pubmed:36035779
description: Object-oriented, webGL based JavaScript library for online molecular visualization – No Java required! With 3Dmol.js, you can add beautifully rendered molecular visualizations to your web applications.
feature list: operation_0570
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.html

3DNALandscapes
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0081
application sub category: topic_0082
application sub category: topic_0166
application sub category: topic_0654
application sub category: topic 3382
citation: pubmed:19906722
description: Database for exploring the conformational features of DNA. It enables searches of conformational information across multiple structures. The database contains a wide variety of structural parameters and molecular images, computed with the 3DNA software package and known to be useful for characterizing and understanding the sequence-dependent spatial arrangements of the DNA sugar-phosphate backbone, sugar-base side groups, base pairs, base-pair steps, groove structure, etc.
feature list: operation_0245
feature list: operation_0339
feature list: operation_0360
feature list: operation 2442
feature list: operation 3431

3DNetMod
type: SoftwareApplication
input: Experimental measurement
  type: FormalParameter
  additional type: data 3108
  encoding format: format 3003
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3176
application sub category: topic 3656
citation: nmeth.4560
citation: pmcid:PMC6029251
citation: pubmed:29334377
description: A package of Python scripts that sensitively detects nested, hierarchical domains in HiC data.
feature list: operation_0279
is accessible for free: true
software help: overview

3DPhenoFish
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0610
application sub category: topic_0621
application sub category: topic 3298
application sub category: topic 3500
application sub category: topic 3810
citation: J.ISSN.2095-8137.2021.141
citation: pmcid:PMC8317184
citation: pubmed:34235898
description: Application for two- and three-dimensional fish morphological phenotype extraction from point cloud analysis.
feature list: operation_0337
feature list: operation 3435
feature list: operation 3891
is accessible for free: true

3DPolyS-LE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic_0654
application sub category: topic 3169
application sub category: topic 3940
citation: btac705
citation: pmcid:PMC9750120
citation: pubmed:36355469
description: An accessible simulation framework to model the interplay between chromatin and loop extrusion.
feature list: operation_0481
is accessible for free: true
license: MIT
operating system: Linux

3DProIN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0128
application sub category: topic_0602
application sub category: topic 2259
citation: ajbcb.2014.1003
citation: pmcid:PMC4316736
citation: pubmed:25664223
description: 3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view.
feature list: operation 3083
operating system: Linux
operating system: Mac
operating system: Windows
software help: UserMenu.pdf

3DRobot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2814
citation: btv601
citation: pmcid:PMC5006309
citation: pubmed:26471454
description: 3DRobot is a program devoted for automated generation of diverse and well-packed protein structure decoys.
feature list: operation 2479
operating system: Linux
software help: about.html

3DRS
type: SoftwareApplication
input: Trajectory data
  type: FormalParameter
  additional type: data 3870
  encoding format: format 3650
  encoding format: format 3875
  encoding format: format 3885
  encoding format: format 3910
input: Nucleic acid structure
  type: FormalParameter
  additional type: data 1459
  encoding format: format 1476
input: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1476
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0081
application sub category: topic_0092
application sub category: topic 1317
application sub category: topic 3307
application sub category: topic 3892
author: Genís Bayarri
contributor: https://orcid.org/0000-0002-8291-8071
description: 3DRS, a web-based tool to share interactive representations of 3D biomolecular structures and Molecular Dynamics trajectories
feature list: operation_0570
feature list: operation 3890
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.html
software version: 1.0

3DSNP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
application sub category: topic_0102
application sub category: topic_0749
application sub category: topic 2885
application sub category: topic 3295
application sub category: topic 3940
citation: GKAB1008
citation: pmcid:PMC8728236
citation: pubmed:34723317
description: 3DSNP is a database linking noncoding Variants to 3D interacting genes. It is an integrated annotation database linking genome-wide noncoding SNPs and small INDELs to 3D interacting genes via chromatin loops.
feature list: operation_0224
feature list: operation 3227
feature list: operation 3431
feature list: operation 3661
software help: 3dsnp-v2-0-api
software help: 3dsnp-v2-0-tutorials
primary contact: https://orcid.org/0000-0001-8005-2705
primary contact: https://orcid.org/0000-0002-4895-5063

3DSpectra
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3344
application sub category: topic 3520
description: A 3-dimensional quantification algorithm for LC–MS labeled profile data
feature list: operation_0314
feature list: operation 3755
feature list: operation 3799
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: Sara Nasso

3DSS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0166
application sub category: topic_0736
application sub category: topic 2814
citation: gkl036
citation: pmcid:PMC1538824
citation: pubmed:16844975
description: Tool for superposing two or more protein structures that uses RASMOL for visualization, some browser configuration is necessary.
feature list: operation_0320
feature list: operation_0321
feature list: operation_0474
feature list: operation_0477
feature list: operation 2406
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.shtml
primary contact: K Sekar

3DTF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0749
application sub category: topic 3125
application sub category: topic 3511
application sub category: topic 3534
citation: gks551
citation: pmcid:PMC3394331
citation: pubmed:22693215
description: 3D Transcription Factor (3DTF) is a web-server for the analysis of protein-DNA binding sites. It calculates the positional weight matrix (PWM), representing the DNA-binding specifity of the protein.
feature list: operation_0389
feature list: operation_0445
feature list: operation_0477
feature list: operation 2575
feature list: operation 3222
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Denitsa Alamanova

3DVizSNP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0081
application sub category: topic_0625
application sub category: topic 2533
application sub category: topic 2885
application sub category: topic 3168
citation: s12859-023-05370-5
citation: pmcid:PMC10251577
citation: pubmed:37296383
description: Tool for rapidly visualizing missense mutations identified in high throughput experiments in iCn3D.
feature list: operation_0302
feature list: operation_0331
feature list: operation_0337
feature list: operation 3227
feature list: operation 3661
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

3FunMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic 3053
citation: btr306
citation: pubmed:21586519
description: It can be used to construct genetic linkage maps and perform functional QTL mapping with molecular markers generated in a full-sib family. For linkage analysis, it utilizes seven segregation types of markers to estimate the recombination and simultaneously predict the linkage phase between any two markers. It takes heuristic search method for ordering large number of markers of a linkage group by incorporating local ordering methods.
feature list: operation_0282
feature list: operation_0283
feature list: operation 2421
feature list: operation 2429
operating system: Windows
software help: 3funmap intro.pdf
software version: 1.0

3GOLD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0080
application sub category: topic_0199
application sub category: topic 3168
application sub category: topic 3315
citation: S12859-022-04637-7
citation: pmcid:PMC8934446
citation: pubmed:35307007
description: Optimized Levenshtein distance for clustering third-generation sequencing data.
feature list: operation_0491
feature list: operation 3096
feature list: operation 3432
license: Not licensed
operating system: Linux
operating system: Mac

3M-SARS-CoV-2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0634
application sub category: topic 2830
application sub category: topic 3930
application sub category: topic 3948
citation: https://doi.org/10.1101/2020.11.12.344424
description: Prediction of potentially immunopathogenic SARS-CoV-2 epitopes via a novel immunoinformatic approach. Choose FASTA files for Peptide Vaccine Candidate Inputs. Load Peptide Vaccine Candidates from OptiVax. Liu, G., Carter, B., Bricken, T., Jain, S., Viard, M., Carrington, M., & Gifford, D. K. (2020). Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions. Cell systems, 11(2), 131–144.e6.
feature list: operation_0249
feature list: operation_0252
feature list: operation_0416
feature list: operation_0477
feature list: operation 3454

3Matrix
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0080
application sub category: topic_0123
application sub category: topic_0160
application sub category: topic 3510
citation: gkg564
citation: pmcid:PMC168971
citation: pubmed:12824319
description: 3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.
feature list: operation_0238
feature list: operation_0239
feature list: operation_0240
feature list: operation_0250
feature list: operation 2404
operating system: Linux
operating system: Mac
software help: 3matrix
primary contact: Douglas L. Brutlag

3MCor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic 3172
application sub category: topic 3174
application sub category: topic 3697
citation: V1
description: The metabolome-microbiome-metadata correlation analysis platform (3MCor) is a web server for integrative correlation analysis of metabolome and microbiome under the instruction of phenotype and with the consideration of confounders. 3MCor is independent to measurement platforms. Along with integrative correlation analysis of metabolome and microbiome under the instruction of metadata (phenotypes and confounders).
feature list: operation 2937
feature list: operation 3463
feature list: operation 3659
feature list: operation 3766
feature list: operation 3797
software help: manual.html
software help: manual1.html
primary contact: https://orcid.org/0000-0003-4163-1098

3Mint
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0659
application sub category: topic 3295
application sub category: topic 3360
application sub category: topic 3474
application sub category: topic 3512
citation: fgene.2023.1093326
citation: pmcid:PMC10050723
citation: pubmed:37007972
description: Feature grouping and scoring in multi-omics.
feature list: operation_0314
feature list: operation_0463
feature list: operation 3792
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

3Motif
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0080
application sub category: topic_0123
application sub category: topic_0160
application sub category: topic_0166
citation: btf862
citation: gkg564
citation: pmcid:PMC168971
citation: pubmed:12611811
citation: pubmed:12824319
description: 3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.
feature list: operation_0238
feature list: operation_0240
feature list: operation_0245
feature list: operation_0250
feature list: operation 2404
operating system: Linux
operating system: Mac
software help: 3motif
primary contact: Douglas L. Brutlag

3Omics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0092
application sub category: topic_0121
application sub category: topic 2259
application sub category: topic 2815
application sub category: topic 3172
application sub category: topic 3308
citation: https://doi.org/10.1186/1752-0509-7-64
citation: pmcid:PMC3723580
citation: pubmed:23875761
description: A web based systems biology visualization tool for integrating human transcriptomic, proteomic and metabolomic data.
feature list: operation 2403
feature list: operation 3208
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
primary contact: Yufeng Jane Tseng

3SEQ_2D
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0654
citation: cmb.2010.0103
citation: pmcid:PMC3122931
citation: pubmed:20874409
description: Software for detecting gene conversion events in whole genomes.
feature list: operation 3434
operating system: Linux
software help: lav format.html

3USS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0077
application sub category: topic_0099
application sub category: topic_0622
application sub category: topic 3170
citation: btv035
citation: pmcid:PMC4443675
citation: pubmed:25617413
description: Web-server developed with the aim of retrieving 3’UTR genomic coordinates and nucleotide sequences of the transcripts assembled by standard RNA-seq analysis protocols.
feature list: operation 2422
feature list: operation 2478
feature list: operation 3680
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
primary contact: Biocomputing Group

3V
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0097
application sub category: topic_0099
application sub category: topic_0166
application sub category: topic_0632
application sub category: topic 3382
citation: gkq395
citation: pmcid:PMC2896178
citation: pubmed:20478824
description: The 3V web server extracts and analyzes all of the internal volumes from input RNA and protein structures. Output is volumetric representations in images and downloadable files.
feature list: operation_0250
feature list: operation_0321
feature list: operation_0387
feature list: operation 2406
feature list: operation 3443
operating system: Linux
operating system: Mac
operating system: Windows
software help: glossary.php
primary contact: R. Neil

4DGenome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3173
application sub category: topic 3656
citation: btv158
citation: pmcid:PMC4514924
citation: pubmed:25788621
description: Curated database of chromatin interaction data covering five organisms: Homo sapiens, Mus musculus, Drosophila melanogaster, Plasmodium falciparum, and Saccharomyces cerevisiae.
feature list: operation_0224
is accessible for free: true
license: CC-BY-NC-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: About.html

4acCPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0160
application sub category: topic_0203
application sub category: topic 3295
application sub category: topic 3474
application sub category: topic 3674
citation: j.omtn.2022.10.004
citation: pmcid:PMC9636570
citation: pubmed:36381577
description: Weakly supervised prediction of N4-acetyldeoxycytosine DNA modification from sequences
feature list: operation_0238
feature list: operation_0417
feature list: operation 3435
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

4D-FED-GNN++
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Workbench
application sub category: topic 3299
citation: TMI.2022.3225083
citation: pubmed:36441899
description: Federated Brain Graph Evolution Prediction using Decentralized Connectivity Datasets with Temporally-varying Acquisitions.
feature list: operation 3436
license: Not licensed
operating system: Windows

4D Nucleome Data Portal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
additional type: Web API
application sub category: topic_0621
application sub category: topic_0654
application sub category: topic 3173
application sub category: topic 3382
application sub category: topic 3940
citation: https://doi.org/10.1101/2021.10.14.464435
description: 4D Nucleome Data Portal is a resource for searching and visualizing curated nucleomics data. The 4D Nucleome program aims to understand the principles behind the 3D organization of the nucleus in space and time (the 4th dimension). The 4DN Data Visualization Workspace allows users to create 1D or 2D genome displays. Registered users can save and share the displays they create. The Visualization Workspace is powered by HiGlass. The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization.
feature list: operation_0337
feature list: operation 2421
feature list: operation 3431
feature list: operation 3454
is accessible for free: true
software help: faq
software help: getting-started
software help: programmatic-access
primary contact: 0000-0001-9378-960X

4DNvestigator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic_0654
application sub category: topic 3170
application sub category: topic 3940
citation: https://doi.org/10.1101/2020.01.08.898387
description: The 4DNvestigator is a MATLAB toolbox that analyzes time-series genome-wide chromosome conformation capture (Hi-C) and gene expression (RNA-seq) data.
feature list: operation_0337
feature list: operation 3565
feature list: operation 3927
license: MIT
operating system: Windows

4DR-GAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0108
application sub category: topic 3382
application sub category: topic 3474
citation: btac719
citation: pmcid:PMC9805574
citation: pubmed:36373962
description: Digitally Predicting Protein Localization and Manipulating Protein Activity in Fluorescence Images Using Four-dimensional Reslicing GAN.
feature list: operation_0477
feature list: operation 2489
feature list: operation 3927
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

4DRoot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0780
application sub category: topic 3298
application sub category: topic 3444
application sub category: topic 3452
application sub category: topic 3810
citation: fpls.2022.986856
citation: pmcid:PMC9539560
citation: pubmed:36212319
description: A spatial–temporal root architectural modeling method based on 4D data from X-ray Computed Tomography (CT) by cylindrical fitting
feature list: operation_0282
feature list: operation_0337
feature list: operation 3435
is accessible for free: true
license: Not licensed

4DXpress
type: SoftwareApplication
input: Gene symbol
  type: FormalParameter
  additional type: data 1026
input: Ensembl gene ID
  type: FormalParameter
  additional type: data 1033
input: Gene ID (FlyBase)
  type: FormalParameter
  additional type: data 1796
output: Gene report
  type: FormalParameter
  additional type: data_0916
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0623
citation: gkm797
citation: pmcid:PMC2238840
citation: pubmed:17916571
description: A platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments.
feature list: operation_0224
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL
software help: help.do
primary contact: Yannick Haudry

4mCpred-EL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3474
citation: CELLS8111332
citation: pmcid:PMC6912380
citation: pubmed:31661923
description: A web application for identification of DNA N4-methylcytosine sites in the mouse genome.
feature list: operation 3435

4mC-w2vec
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3474
citation: J.CSBJ.2021.03.015
citation: pmcid:PMC8042287
citation: pubmed:33868598
description: 4mC-w2vec is a web tool for identifying DNA N4-methylcytosine sites in the rosaceae genome with a deep learning model relying on distributed feature representation.
primary contact: Kil To Chong

4mcPred-IFL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0749
application sub category: topic 3295
application sub category: topic 3474
citation: BTZ408
citation: pubmed:31099381
description: Generic webserver for predicting N4-methylcytosine (4mC) sites.
feature list: operation_0417
feature list: operation 3896
feature list: operation 3897
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: home.html
primary contact: Leyi Wei
primary contact: Shasha Luan

4mCNLP-Deep
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3474
citation: S41598-020-80430-X
citation: pmcid:PMC7794489
citation: pubmed:33420191
description: 4mCNLP-Deep is a tool the identification of N4-methylcytosine. It performs natural language processing by exploiting deep learning algorithm.

4peaks
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3168
description: Allows viewing sequencing trace files, motif searching trimming, BLAST and exporting sequences.
feature list: operation 2403
operating system: Mac
primary contact: Bug Report
primary contact: Support

4Pipe4
type: SoftwareApplication
input: Sequence set (nucleic acid)
  type: FormalParameter
  additional type: data 1234
  encoding format: format 2330
  encoding format: format 3284
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0077
application sub category: topic_0080
application sub category: topic 2885
citation: s12859-016-0892-1
citation: pmcid:PMC4719533
citation: pubmed:26787189
description: A pipeline with emphasis on SNP detection. It will detect SNPs in NGS data where no reference sequence nor strain information is available.
feature list: operation_0484
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: 4Pipe4
software version: 1.7.1
primary contact: Francisco Pina Martins

4SALE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0080
application sub category: topic_0081
application sub category: topic_0099
citation: https://doi.org/10.1186/1756-0500-1-91
description: 4SALE allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis.
feature list: operation_0295
feature list: operation 2480
feature list: operation 3096
operating system: Linux
operating system: Mac
operating system: Windows
software help: help 1.html
software version: 1.7

4See
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0204
application sub category: topic_0749
application sub category: topic 3173
application sub category: topic 3512
application sub category: topic 3940
citation: FGENE.2019.01372
citation: pmcid:PMC6985583
citation: pubmed:32038719
description: A Flexible Browser to Explore 4C Data.
feature list: operation_0337
feature list: operation 3192
feature list: operation 3435
license: GPL-3.0
software help: 4See manual.pdf

4SpecID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0654
application sub category: topic 3053
citation: GENES12010061
citation: pmcid:PMC7824288
citation: pubmed:33401773
description: 4SpecID is a cross-platform program to audit and annotate reference DNA libraries. It is oriented to ensure the golden standards for forensic applications.
feature list: operation_0291
feature list: operation_0361
feature list: operation 3460
feature list: operation 3894
operating system: Linux
operating system: Mac
operating system: Windows

5PSeq Explorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Web-based platform for interactive exploration of ribosome dynamics derived from 5′P mRNA degradome sequencing (5PSeq) data. Focused on changes in ribosome dynamics associated to mRNA decay that in some cases can be obscured in conventional ribosome profiling data.
software version: 1.3

5_ORF_Extender
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3512
citation: s00335-013-9498-3
citation: j.ygeno.2012.05.012
citation: ijmm.2017.2942
citation: pubmed:22659028
citation: pubmed:24504701
citation: pubmed:28393177
description: '5'_ORF_Extender' is a tool that can perform a systematic identification of extended coding regions (CDS) at the 5´ end of known mRNAs, using an EST-based approach.
operating system: Mac
operating system: Windows
software help: 5' ORF Extender 2 Tutorial.html
software version: 2.0.1

5NosoAE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0084
application sub category: topic 3305
application sub category: topic 3324
application sub category: topic 3810
citation: gkac423
citation: pmcid:PMC9252726
citation: pubmed:35639518
description: A web server for nosocomial bacterial antibiogram investigation and epidemiology survey.
feature list: operation_0337
feature list: operation 2421
feature list: operation 3482
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

6mA-Finder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0654
application sub category: topic 2640
application sub category: topic 3295
citation: BTAA113
citation: pmcid:PMC7214014
citation: pubmed:32091591
description: A novel online tool for predicting DNA N6-methyladenine sites in genomes.
is accessible for free: true

6mA-Pred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3295
citation: PEERJ.10813
citation: pmcid:PMC7866889
citation: pubmed:33604189
description: 6mA-Pred is a web tool for identifying DNA N6-methyladenine sites based on deep learning.
feature list: operation 3937

6mAPred-FO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0654
application sub category: topic_0780
application sub category: topic 3295
application sub category: topic 3474
application sub category: topic 3674
citation: FBIOE.2020.00502
citation: pmcid:PMC7287168
citation: pubmed:32582654
description: A Bioinformatics Tool for the Prediction of DNA N6-Methyladenine Modifications Based on Feature Fusion and Optimization Protocol.
feature list: operation 3454
feature list: operation 3927
feature list: operation 3936
is accessible for free: true

959 Nematode Genomes
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0080
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic 3168
application sub category: topic 3500
citation: gkr826
citation: pmcid:PMC3245058
citation: pubmed:22058131
description: A community-curated semantic wiki to coordinate the sequencing efforts of individual labs to collectively sequence 959 genomes spanning the phylum Nematoda. The main goal of the wiki is to track sequencing projects that have been proposed, are in progress, or have been completed.
feature list: operation_0224
feature list: operation_0362
feature list: operation_0525
feature list: operation 3196
feature list: operation 3267
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Mark Blaxter

9aaTAD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0621
application sub category: topic_0749
application sub category: topic 2229
application sub category: topic 3512
citation: https://doi.org/10.1101/2019.12.15.876706
description: A web application for predicting 9aaTAD activation domains in a sequence.
feature list: operation_0303
feature list: operation_0445
feature list: operation 3216

A-Lister
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0108
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3170
citation: S12859-019-3121-X
citation: pmcid:PMC6862834
citation: pubmed:31744472
description: A tool for analysis of differentially expressed omics entities across multiple pairwise comparisons.
feature list: operation_0315
feature list: operation 3695
feature list: operation 3741
license: MIT

AAI-profiler
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
description: AAI-profiler [1] is a fast homology search tool that takes a query proteome (protein sequences in FASTA format) as input and plots the AAI (Average Amino-acid Identity) values of species in the Uniprot database. AAI-profiler is powered by SANS [2] and the processing time for a bacterial proteome is a few minutes.
feature list: operation_0224

AAScatterPlot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0123
application sub category: topic_0199
application sub category: topic 3534
citation: btx203
citation: pmcid:PMC5859973
citation: pubmed:28383669
description: Tool for looking at aligned nucleotide and amino acid sequences to observe variations in hydropathy index, volume, and charge of residues of a protein.
feature list: operation_0490
feature list: operation 2940
feature list: operation 3192
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software version: 1.0
primary contact: Gary R. Whittaker

Antibodies Chemically Defined Database (ABCD)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0749
application sub category: topic 2830
citation: GKZ714
citation: pubmed:31410491
description: A database for chemically defined antibodies.
feature list: operation 3431

ABCharge
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0593
citation: ACSOMEGA.9B00270
citation: pmcid:PMC6648237
citation: pubmed:31459783
description: An R package to calculate equilibirum conditions with and without correction for ionic strength using Davies' equation.

ABI software
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3334
description: Experimental Brain Computer Interface Software for the ModularEEG.
is accessible for free: true
license: Unlicense
operating system: Windows
primary contact: Jim Peters
primary contact: Pedro Ortega

ABMDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 2640
citation: BTZ297
citation: pubmed:31038664
description: Adaptive boosting-based computational model for predicting potential miRNA-disease associations.
feature list: operation_0463
feature list: operation 3792
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Windows
primary contact: Xing Chen

ABPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3408
application sub category: topic 3474
citation: fphys.2018.01638
citation: pmcid:PMC6258961
citation: pubmed:30519191
description: R Package for Calculating the Abnormal Blood Profile Score.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ABPS.pdf
primary contact: Frédéric Schütz

ABRicate
type: SoftwareApplication
input: Sequence set (nucleic acid)
  type: FormalParameter
  additional type: data 1234
  encoding format: format 1929
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1927
  encoding format: format 1929
  encoding format: format 1936
output: Gene report
  type: FormalParameter
  additional type: data_0916
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0622
application sub category: topic 3301
author: 0000-0001-6046-610X
description: Mass screening of contigs for antimicrobial resistance or virulence genes.
feature list: operation 3482
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
software help: README.md
software version: 0.9.8

Accessory-based source attribution (AB_SA)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 2885
application sub category: topic 3305
application sub category: topic 3500
application sub category: topic 3697
citation: mgen.0.000366
citation: https://doi.org/10.1101/814459
citation: pmcid:PMC7478624
citation: pubmed:32320376
description: The Accessory-based source attribution (AB_SA) method aims at attributing the origin of bacterial strains associated to human cases or isolated in environment.
feature list: operation 3192
feature list: operation 3659
feature list: operation 3791
feature list: operation 3840
license: GPL-3.0

ACACIA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic_0632
application sub category: topic 3168
citation: https://doi.org/10.1101/638288
description: Allele CAlling proCedure for Illumina Amplicon sequencing data.
feature list: operation_0308
feature list: operation 3196
feature list: operation 3227
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Pablo S.C. Santos

ACCOST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic 3169
application sub category: topic 3295
citation: gkaa069
citation: pmcid:PMC7049724
citation: pubmed:32034421
description: ACCOST is a Python script that assigns statistical significance to differences in contact counts in Hi-C experiment.
license: Apache-2.0

ACES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0625
application sub category: topic 3295
application sub category: topic 3474
citation: s12864-018-5300-y
citation: pmcid:PMC6307290
citation: pubmed:30587115
description: Machine learning toolbox for clustering analysis and visualization.
feature list: operation 2939
feature list: operation 3432
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ACES

ACID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic_0209
application sub category: topic 2275
application sub category: topic 3373
citation: s13321-019-0394-z
citation: pmcid:PMC6882193
citation: pubmed:33430982
description: A free tool for drug repurposing using consensus inverse docking strategy.
feature list: operation_0337
feature list: operation_0482
feature list: operation 3899
is accessible for free: true

ACPP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
author: https://orcid.org/0000-0001-5145-0384
citation: s10989-014-9435-7
description: ACPP is a Support Vector Machine based tool to predict whether the given peptide is an Anti-cancer peptide or Not. The three different modes include (i) Protein scan with apoptotic domain prediction; (ii) Multiple peptide mode; and (iii) Peptide mutation mode for prediction and design of anti-cancer peptides. Refer: "ACPP: A Web Server for Prediction and Design of Anti-cancer Peptides." International Journal of Peptide Research and Therapeutics 21.1 (2015): 99-106" for more deatils.
feature list: operation 2423
is accessible for free: true
license: GPL-3.0
operating system: Linux

ACPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0749
application sub category: topic 3474
citation: MOLECULES24101973
citation: pmcid:PMC6571645
citation: pubmed:31121946
description: Computational Tool for the Prediction and Analysis of Anticancer Peptides.
feature list: operation_0252
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

ACPred-Fuse
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3474
citation: BBZ088
citation: pubmed:31729528
description: ACPred-Fuse is a web application that automatically can predict protein sequences with or without anticancer activity in peptide form.
feature list: operation 3092
feature list: operation 3631
feature list: operation 3767

Atlas of Cancer Signalling Network (ACSN)
type: SoftwareApplication
input: Pathway or network
  type: FormalParameter
  additional type: data 2600
input: Gene expression profile
  type: FormalParameter
  additional type: data_0928
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 3047
application sub category: topic 3474
citation: j.patter.2021.100270
citation: pmcid:PMC8212143
citation: pubmed:34179848
description: A multi-scale resource of biological maps to study disease mechanisms.
feature list: operation_0314
feature list: operation_0315
feature list: operation_0533
feature list: operation 2436
feature list: operation 3927
feature list: operation 3935

ACTINN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3474
citation: BTZ592
citation: pubmed:31359028
description: Automated Identification of Cell Types in Single Cell RNA Sequencing | Automated Cell Type Identification using Neural Networks | ACTINN (Automated Cell Type Identification using Neural Networks) is a bioinformatic tool to quickly and accurately identify cell types in scRNA-Seq. For details, please read the paper: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz592/5540320 All datasets used in the paper are available here: https://figshare.com/articles/ACTINN/8967116
feature list: operation 3891

ACTOR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0634
application sub category: topic 3170
application sub category: topic 3334
application sub category: topic 3512
citation: https://doi.org/10.1101/856401
description: a latent Dirichlet model to compare expressed isoform proportions to a reference panel. actor is an R package which takes transcript expression as input and uses a latent Dirichlet model to compare to GTEx tissues. actor provides gene level similarities to the GTEx tissues and identifies collections of genes, or gene classes, which align similarly to GTEx tissues
feature list: operation 2499
feature list: operation 3196
feature list: operation 3658

ACTman
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0769
citation: J.JSAMS.2019.11.009
citation: pubmed:31813761
description: Automated preprocessing and analysis of actigraphy data. OBJECTIVES:To introduce a novel software-library called Actigraphy Manager (ACTman) which automates labor-intensive actigraphy data preprocessing and analyses steps while improving transparency, reproducibility, and scalability over software suites traditionally used in actigraphy research practice. DESIGN:Descriptive. METHODS:Use cases are described for performing a common actigraphy task in ACTman and alternative actigraphy software. Important inefficiencies in actigraphy workflow are identified and their consequences are described. We explain how these hinder the feasibility of conducting studies with large groups of athletes and or longer data collection periods. Thereafter, the information flow through the ACTman software is described and we explain how it alleviates aforementioned inefficiencies.

ADAPTABLE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3168
citation: LSA.201900512
citation: pmcid:PMC6864362
citation: pubmed:31740563
description: A comprehensive web platform of antimicrobial peptides tailored to the user's research. Antimicrobial peptides (AMPs) are part of the innate immune response to pathogens in all of the kingdoms of life. They have received significant attention because of their extraordinary variety of activities, in particular, as candidate drugs against the threat of super-bacteria.
feature list: operation_0491
feature list: operation 3216
feature list: operation 3802

ADAPTIVE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3474
citation: btz319
citation: pmcid:PMC6612897
citation: pubmed:31510641
description: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra | Learning molecular vectors for metabolites from spectra-structure pairs] | We propose ADAPTIVE, which has two parts: learning two mappings 1) from structures to molecular vectors and 2) from spectra to molecular vectors
feature list: operation 3627
feature list: operation 3803
feature list: operation 3860

ADAPTS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3518
citation: https://doi.org/10.1101/633958
description: Automated Deconvolution Augmentation of Profiles for Tissue Specific cells.
feature list: operation 2495
feature list: operation 3237
feature list: operation 3629
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: ADAPTS.pdf
primary contact: Samuel A. Danziger

ADDO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic 2885
application sub category: topic 3517
citation: BTZ786
citation: pubmed:31764991
description: a comprehensive toolkit to detect, classify and visualise additive and non-additive Quantitative Trait Loci. We developed ADDO, a highly-efficient tool designed to detect, classify and visualize quantitative trait loci (QTLs) with additive and non-additive effects. ADDO implements a mixed-model transformation to control for population structure and unequal relatedness that accounts for both additive and dominant genetic covariance among individuals, and decomposes single nucleotide polymorphism (SNP) effects into additive, partial dominance, dominance and overdominance categories. A matrix multiplication approach is used to accelerate the computation: a genome scan on 20 million markers from 836 individuals takes about 8.5 hours with 10 CPUs. Additivity and dominance are the major genetic components underlying variations in complex traits
feature list: operation_0282
feature list: operation 3196
feature list: operation 3799
license: LGPL-3.0

ADEPTUS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic_0634
citation: bty027
citation: pubmed:29360930
description: Discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases.
feature list: operation 2495
feature list: operation 3501
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorials
primary contact: Ron Shamir

ADHD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3305
application sub category: topic 3334
application sub category: topic 3419
citation: s2045796019000283
citation: pmcid:PMC8061253
citation: pubmed:31088588
description: Risk calculator to predict ADHD in young adulthood.
feature list: operation 3435
feature list: operation 3557
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

ADMMBO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 2269
citation: pmcid:PMC6890416
citation: pubmed:31798351
description: Bayesian Optimization with Unknown Constraints using ADMM. There exist many problems in science and engineering that involve optimization of an unknown or partially unknown objective function. Recently, Bayesian Optimization (BO) has emerged as a powerful tool for solving optimization problems whose objective functions are only available as a black box and are expensive to evaluate. Many practical problems, however, involve optimization of an unknown objective function subject to unknown constraints. This is an important yet challenging problem for which, unlike optimizing an unknown function, existing methods face several limitations. In this paper, we present a novel constrained Bayesian optimization framework to optimize an unknown objective function subject to unknown constraints.

ADRAlert
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0202
application sub category: topic_0209
application sub category: topic 3377
application sub category: topic 3379
application sub category: topic 3474
citation: cpt.1750
citation: bbz140
citation: pmcid:PMC7325315
citation: pubmed:31838499
citation: pubmed:31868917
description: Broad-Spectrum Profiling of Drug Safety via Learning Complex Network.
feature list: operation_0478
feature list: operation 2426
feature list: operation 3435
feature list: operation 3439

ADS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0089
application sub category: topic_0091
application sub category: topic 3474
citation: JOURNAL.PCBI.1007419
citation: pmcid:PMC6855565
citation: pubmed:31682632
description: A novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
feature list: operation 2940
feature list: operation 3352
feature list: operation 3778

ADS-HCSpark
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3303
citation: s12859-019-2665-0
citation: pmcid:PMC6376756
citation: pubmed:30764760
description: Scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark.
feature list: operation 3196
feature list: operation 3227
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
software help: README.md

AEnet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: We construct a novel method named alternative splicing network(AEN) combining gene expression levels with AS patterns to analyze cellular heterogeneity, identify novel cell types, and infer the regulatory mechanisms of alternative splicing. By applying the AEN method to gastrula data, pan-cancer T-cell data, and lung cancer tumor cell data, we have successfully revealed the hidden alternative splicing heterogeneity in these cells and identified key alternative splicing events and related splicing factors during cell transformation. The application of AEN method provides new insights into the understanding of cellular heterogeneity and its related physiological and pathological processes.
feature list: operation 2499
feature list: operation 2844
software version: version1.1

Advanced Expression Survival Analysis (AESA)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1080/15476286.2019.1679585
citation: pmcid:PMC7567505
citation: pubmed:31607216
description: A web tool which provides several novel survival analysis approaches. It computes the gene expression composite score of a set of genes for survival analysis and utilizes permutation test or cross-validation to assess the significance of log-rank statistic and the degree of over-fitting.
feature list: operation 2495
feature list: operation 3435

AFCMHeatMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic 3169
application sub category: topic 3170
application sub category: topic 3518
citation: PEERJ.PREPRINTS.2961V2
description: A shiny web tool for heatmap generation of genetic expression datasets using R packages. Generating heatmaps of genetic datasets is a 2D graphical visualization of data where the individual expression values contained in a matrix are represented as colors. Herein, we describe AFCMHeatMap a shiny web App that integrates quantitative interaction of genomics data and results from microarrays or RNA-Seq to highlight expression levels of various genetic datasets with a *.CSV input file. The application also facilitates downloading heatmaps as a supplementary material for user's publications. Written in R using Shiny framework, it is a user-friendly framework for interactive expression data visualization that can be easily deployed without any restrictions to any operating system used by any online user
feature list: operation_0531
feature list: operation 2938
feature list: operation 3435
feature list: operation 3800
license: GPL-3.0

The Allele Frequency Net Database (AFND)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0208
application sub category: topic_0625
application sub category: topic 2830
citation: GKZ1029
citation: pubmed:31722398
description: The Allele Frequency Net Database (AFND) provides the scientific community with a freely available repository for the storage of frequency data (alleles, genes, haplotypes and genotypes) related to human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors (KIR), major histocompatibility complex Class I chain related genes (MIC) and a number of cytokine gene polymorphisms in worldwide populations.
feature list: operation_0224
feature list: operation 3196
feature list: operation 3431

AGAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0622
citation: zenodo.3552717
description: Another Gff Analysis Toolkit (AGAT) Suite of tools to handle gene annotations in any GTF/GFF format.
feature list: operation_0362
feature list: operation 2409
is accessible for free: true
license: GPL-3.0
software help: AGAT
software version: v0.1.0

AGONOTES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0621
application sub category: topic_0736
application sub category: topic 3912
citation: S12539-019-00349-4
citation: pubmed:31741225
description: A Robot Annotator for Argonaute Proteins. Welcome to AgoNotes home page! AGONOTES is an online service tool to identify Argonaute protein in proteins of all domains of life and annotate the argonaute domains. Users can submit any protein with fasta formation into the input field, or save proteins as a file ended with .faa, .fasta, .fa or .txt and then upload this file
feature list: operation_0224
feature list: operation_0362
feature list: operation 3096

AGS ACN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3174
application sub category: topic 3399
application sub category: topic 3697
citation: S12859-019-3031-Y
citation: pmcid:PMC6727555
citation: pubmed:31488068
description: > CORRECT NAME OF TOOL COULD ALSO BE 'ags.sh acn.sh tools', 'AGS', 'ACN' | Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data | Here, we present the ags.sh and acn.sh tools dedicated to the computation of the Average Genome Size (AGS) and 16S rRNA gene Average Copy Number (ACN), respectively. The ags.sh and acn.sh tools compute these metagenomic traits based on the (ultra-fast) annotation of 35 universally distributed single-copy genes in unassembled metagenomic data | Pereira-Flores, E., Glöckner F. O., and Fernandez-Guerra A. Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data. BMC Bioinformatics. 2019;20(1):453. doi:10.1186/s12859-019-3031-y
feature list: operation_0310
feature list: operation_0362
feature list: operation 2495
license: GPL-3.0

AICD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3336
application sub category: topic 3375
citation: S41598-019-44227-X
citation: pmcid:PMC6533287
citation: pubmed:31123286
description: Anti-Inflamamtory Compounds Database for drug discovery.
feature list: operation 2939
feature list: operation 3431
feature list: operation 3891
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: about.php
primary contact: Biaoyan Du
primary contact: Jiangyong Gu
primary contact: Zaoyuan Kuang

AIDE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: GR.251108.119
citation: pmcid:PMC6886511
citation: pubmed:31694868
description: annotation-assisted isoform discovery with high precision. AIDE: annotation-assisted isoform discovery and quantification from RNA-seq data. AIDE is a statistical method which identifies full-length mRNA isoforms from a novel perspective: using the likelihood ratio test to find novel isoforms in a stepwise manner given annotated isoforms, by prioritizing and selectively borrowing information from the annotated isoforms. Please refer to our preprint at Biorxiv for detailed description of our method
feature list: operation_0264
feature list: operation_0524
feature list: operation 3800

AIKYATAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3173
application sub category: topic 3474
citation: S12859-019-3049-1
citation: pmcid:PMC6781298
citation: pubmed:31590652
description: mapping distal regulatory elements using convolutional learning on GPU. BACKGROUND:The data deluge can leverage sophisticated ML techniques for functionally annotating the regulatory non-coding genome. The challenge lies in selecting the appropriate classifier for the specific functional annotation problem, within the bounds of the hardware constraints and the model's complexity. In our system AIKYATAN, we annotate distal epigenomic regulatory sites, e.g., enhancers. Specifically, we develop a binary classifier that classifies genome sequences as distal regulatory regions or not, given their histone modifications' combinatorial signatures. This problem is challenging because the regulatory regions are distal to the genes, with diverse signatures across classes (e.g., enhancers and insulators) and even within each class (e.g., different enhancer sub-classes)
feature list: operation_0417
feature list: operation_0438
feature list: operation 3443

AIVAR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 3474
application sub category: topic 3676
citation: BTZ442
citation: pubmed:31141141
description: Assessing concordance among human, in silico predictions and functional assays on genetic variant classification.
feature list: operation 3225
feature list: operation 3431
feature list: operation 3461
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Jianfeng Sang
primary contact: Jiaqi Luo
primary contact: Yujian Shi

AI TI-RADS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3384
application sub category: topic 3474
citation: RADIOL.2019182128
citation: pubmed:31112088
description: Interactive calculator for Artificial Intelligence (AI) Thyroid Imaging Reporting and Data System (TI-RADS).
is accessible for free: true
license: CC-BY-NC-SA-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Mateusz Buda

AJIA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0089
application sub category: topic_0102
application sub category: topic 3168
citation: TCBB.2019.2951137
citation: pubmed:31689201
description: Jointly integrating VCF-based variants and OWL-based biomedical ontologies in MongoDB.
feature list: operation 3227

ALACD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3512
citation: journal.pcbi.1007540
citation: pmcid:PMC6948815
citation: pubmed:31877126
description: Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs. ALACD is to get the drug-lncRNA assoications via bi-level optimization and decoded in R. It includes SVM standard algorithm for argumenting the genes' co-expressed lncRNAs (enhancering-lncRNA-mRNA-coexpression.R), and the optimization procedure for optimal identification of genes aassociated with both lncRNAs and drug to get the drug-lncRNA assoications (optimizating.R). crossvalSVM.R and getperf.R are for SVM cross-validtion and generating the evluation criteria, respectively. It also includes the DEGanalysis.R for differential expression analysis, and survival-analysis.R for surivival analysis of lncRNAs
feature list: operation 2495
feature list: operation 3223
feature list: operation 3557

ALIENNESS
type: SoftwareApplication
input: Gene tree
  type: FormalParameter
  additional type: data 3271
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0194
application sub category: topic 3944
citation: genes8100248
citation: pmcid:PMC5664098
citation: pubmed:28961181
description: Rapid detection of candidate horizontal gene transfers across the tree of life.
feature list: operation 2403
feature list: operation 2451
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

ALOHA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: S12911-019-0857-1
citation: pmcid:PMC6686235
citation: pubmed:31391091
description: > MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | developing an interactive graph-based visualization for dietary supplement knowledge graph through user-centered design | BACKGROUND:Dietary supplements (DSs) are widely used. However, consumers know little about the safety and efficacy of DSs. There is a growing interest in accessing health information online; however, health information, especially online information on DSs, is scattered with varying levels of quality. In our previous work, we prototyped a web application, ALOHA, with interactive graph-based visualization to facilitate consumers' browsing of the integrated DIetary Supplement Knowledge base (iDISK) curated from scientific resources, following an iterative user-centered design (UCD) process. METHODS:Following UCD principles, we carried out two design iterations to enrich the functionalities of ALOHA and enhance its usability
feature list: operation 3501

ALS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic 3474
citation: BTZ369
citation: pmcid:PMC6612814
citation: pubmed:31510706
description: Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype | Deep learning frame for genetic disease | Synthetic data https://drive.google.com/open?id=1Mya0YdT4Hf9wUfbcX6y5mubEFWky6Jg-
feature list: operation 3196
feature list: operation 3557
feature list: operation 3891

ALTIS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3384
application sub category: topic 3421
application sub category: topic 3452
citation: MP.13773
citation: pubmed:31435950
description: PURPOSE:The automated segmentation of each lung and trachea in CT scans is commonly taken as a solved problem. Indeed, existing approaches may easily fail in the presence of some abnormalities caused by a disease, trauma, or previous surgery. For robustness, we present ALTIS (implementation is available at http: lids.ic.unicamp.br downloads) - a fast automatic lung and trachea CT-image segmentation method that relies on image features and relative shape- and intensity-based characteristics less affected by most appearance variations of abnormal lungs and trachea. METHODS:ALTIS consists of a sequence of image foresting transforms (IFTs) organized in three main steps: (a) lung-and-trachea extraction, (b) seed estimation inside background, trachea, left lung, and right lung, and (c) their delineation such that each object is defined by an optimum-path forest rooted at its internal seeds

AMDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
application sub category: topic 3174
application sub category: topic 3697
citation: FGENE.2019.00350
citation: pmcid:PMC6491633
citation: pubmed:31068967
description: Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis.
feature list: operation 3677
feature list: operation 3741
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: AMDA-manual.pdf
primary contact: Xiang Zhan

AMELIE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic 3068
application sub category: topic 3676
citation: https://doi.org/10.1101/839878
description: A web application for automatic mendelian literature evaluation.
feature list: operation 1812
feature list: operation 3196
feature list: operation 3226

AMICI
type: SoftwareApplication
input: Pathway or network
  type: FormalParameter
  additional type: data 2600
  encoding format: format 2585
  encoding format: format 4015
output: Trajectory data
  type: FormalParameter
  additional type: data 3870
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2259
author: https://orcid.org/0000-0001-9963-6057
author: Fabian Fröhlich
citation: btab227
citation: pmcid:PMC8545331
citation: pubmed:33821950
description: AMICI provides a multi-language (Python, C++, Matlab) interface for the SUNDIALS solvers CVODES (for ordinary differential equations) and IDAS (for algebraic differential equations). AMICI allows the user to read differential equation models specified as SBML or PySB and automatically compiles such models into .mex simulation files (Matlab), C++ executables or Python modules. Beyond forward integration, the compiled simulation file also allows for forward sensitivity analysis, steady state sensitivity analysis and adjoint sensitivity analysis for likelihood-based output functions. The interface was designed to provide routines for efficient gradient computation in parameter estimation of biochemical reaction models but it is also applicable to a wider range of differential equation constrained optimization problems.
feature list: operation 2426
feature list: operation 3562
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest
primary contact: https://orcid.org/0000-0001-9963-6057
primary contact: https://orcid.org/0000-0002-4935-3312
primary contact: Fabian Fröhlich

AMON
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3366
application sub category: topic 3572
application sub category: topic 3697
citation: S12859-019-3176-8
citation: pmcid:PMC6883642
citation: pubmed:31779604
description: annotation of metabolite origins via networks to integrate microbiome and metabolome data. Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data. It is recommended to install AMON in a conda environment. The environment can be created by first downloading the environment file. A command line tool for predicting the compounds produced by microbes and the host. AMON includes two scripts. extract_ko_genome_from_organism.py takes a KEGG organism flat file and makes a list of KOs present in that file. AMON.py predicts the metabolites that could be produced by the KOs used as input. This can be compared to the KOs present in the host or from some other gene set as well as to as set of KEGG metabolites
feature list: operation 2436
feature list: operation 3083
feature list: operation 3803
license: MIT

AMR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3301
application sub category: topic 3305
application sub category: topic 3324
application sub category: topic 3572
author: https://orcid.org/0000-0001-7620-1800
citation: https://doi.org/10.1101/810622
contributor: https://orcid.org/0000-0001-5809-5995
description: An R Package for Working with Antimicrobial Resistance Data.
feature list: operation 3482
license: GPL-2.0

AMi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0611
application sub category: topic_0749
application sub category: topic 2828
citation: S2053230X19009853
citation: pmcid:PMC6688666
citation: pubmed:31397323
description: A GUI-based, open-source system for imaging samples in multi-well plates | Described here are instructions for building and using an inexpensive automated microscope (AMi) that has been specifically designed for viewing and imaging the contents of multi-well plates. The X, Y, Z translation stage is controlled through dedicated software (AMiGUI) that is being made freely available. Movements are controlled by an Arduino-based board running grbl, and the graphical user interface and image acquisition are controlled via a Raspberry Pi microcomputer running Python. Images can be written to the Raspberry Pi or to a remote disk. Plates with multiple sample wells at each row column position are supported, and a script file for automated z-stack depth-of-field enhancement is written along with the images
feature list: operation 3552

ANCIS-Pytorch
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 2229
application sub category: topic 3304
application sub category: topic 3474
citation: J.MEDIA.2019.05.004
citation: pubmed:31103790
description: Attentive neural cell instance segmentation.
feature list: operation 3552
is accessible for free: true
license: Unlicense
operating system: Linux
software help: README.md
primary contact: Daniel J. Hoeppner
primary contact: Dimitris N. Metaxas
primary contact: Jingru Yi
primary contact: Menglin Jiang
primary contact: Pengxiang Wu
primary contact: Qiaoying Huang

ANDIS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0130
application sub category: topic_0736
application sub category: topic 3306
citation: s12859-019-2898-y
citation: pmcid:PMC6547486
citation: pubmed:31159742
description: Atomic angle- and distance-dependent statistical potential for protein structure quality assessment.
feature list: operation_0249
feature list: operation_0321
feature list: operation_0476
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

ANISEED
type: SoftwareApplication
input: Evidence
  type: FormalParameter
  additional type: data 2042
  encoding format: format 2330
output: Evidence
  type: FormalParameter
  additional type: data 2042
  encoding format: format 2332
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Ontology
additional type: Web API
additional type: Web application
application sub category: topic_0084
application sub category: topic_0085
application sub category: topic_0089
application sub category: topic_0194
application sub category: topic_0219
application sub category: topic 2229
application sub category: topic 3064
application sub category: topic 3065
application sub category: topic 3308
application sub category: topic 3383
application sub category: topic 3679
citation: j.cub.2005.12.044
citation: gkv966
citation: gkx1108
citation: gkz955
citation: gr.108175.110
description: ANISEED is the main model organism database for the worldwide community of scientists working on tunicates (sister-group of vertebrates). It integrates for each species: i) a main knowledge base with extended functional, gene expression, phenotyping, anatomical and phylogenetic information; ii) A multispecies genomic browser; iii) a Genomicus gene synteny browser.
feature list: operation_0224
feature list: operation_0292
feature list: operation_0336
feature list: operation_0362
feature list: operation_0567
feature list: operation 2478
feature list: operation 2495
feature list: operation 3208
feature list: operation 3431
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: privacyPolicy
software help: termOfUse
software help: api
software version: 2019
primary contact: https://orcid.org/0000-0001-7247-6460
primary contact: https://orcid.org/0000-0003-4925-2009

ANMF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3336
application sub category: topic 3379
application sub category: topic 3474
citation: S12859-019-2983-2
citation: pmcid:PMC6694624
citation: pubmed:31412762
description: Additional Neural Matrix Factorization model for computational drug repositioning | This is our implementation for the paper“Additional Neural Matrix Factorization model for Computational drug repositioning. BMC Bioinformatics ” | This is our implementation for the paper“Additional Neural Matrix Factorization model for Computational drug repositioning. BMC Bioinformatics ” #Author Xin-Xing Yang Southeast University Email:220174323@seu.edu.cn | Open the "ANMF.py" file and run it directly. In the Data folder is the test example we provide | We use Keras with Theano as the backend
feature list: operation 3501

ANN-Glycolysis-Flux-Prediction
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic_0821
application sub category: topic 3474
citation: JOURNAL.PONE.0216178
citation: pmcid:PMC6505829
citation: pubmed:31067238
description: Flux prediction using artificial neural network (ANN) for the upper part of glycolysis.
feature list: operation 3435
feature list: operation 3439
feature list: operation 3715
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-3568-9595

ANN-SoLo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: https://doi.org/10.1101/627497
description: ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching.
feature list: operation 3627
feature list: operation 3755
feature list: operation 3801
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Wout Bittremieux

ANPELA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic 3172
application sub category: topic 3174
citation: bby127
citation: pmcid:PMC7299298
citation: pubmed:30649171
description: Analysis and Performance Assessment of Label-free Proteome Quantification.
feature list: operation 3634
feature list: operation 3638
feature list: operation 3639
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: anpela
primary contact: Feng Zhu
primary contact: Jianbo Fu
primary contact: Jing Tang
primary contact: Yunxia Wang

AOE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3518
citation: https://doi.org/10.1101/626754
description: AOE (All Of gene Expression) - an integrated index for public gene expression databases.
feature list: operation 2422
feature list: operation 2495
feature list: operation 3800
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: 20180818.html
software help: API documentation.md

AOP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 2840
application sub category: topic 3343
citation: EHP5297
citation: pmcid:PMC6791490
citation: pubmed:31487205
description: Opportunities and Challenges with in Vitro Testing and Adverse Outcome Pathway Approaches | Welcome to the Collaborative Adverse Outcome Pathway Wiki (AOP-Wiki) | This wiki is hosted by the Society for the Advancement of Adverse Outcome Pathways (SAAOP) and serves as one component of a larger OECD-sponsored AOP Knowledgebase (AOP-KB) effort. The AOP-KB represents the central repository for all AOPs developed as part of the OECD AOP Development Effort by the Extended Advisory Group on Molecular Screening and Toxicogenomics. All AOPs from the AOP Knowledgebase are available via the e.AOP.Portal, which is the primary entry point for the AOP-KB. More information about the AOP-KB efforts, the organizations supporting these efforts, and the other modules of the AOP-KB are available on the About page

AOPERA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 2840
application sub category: topic 3314
citation: ALTEX.1906201
citation: pubmed:31453632
description: A proposed methodology and inventory of effective tools to link chemicals to adverse outcome pathways | Welcome to the Adverse Outcome Pathway Exploratory Research Assistant (AOPERA)! | AOPERA is designed to identify existing tools that can assist you in the process of linking your chemical to an adverse outcome pathway (AOP). This informational tool is specifically targeted to users with an uncharacterized chemical and limited toxicity information, but can also assist you if you already have information that links your uncharacterized chemical to a molecular initiating event (MIE), a key event (KE), or an adverse outcome (AO), or if you have a characterized chemical
feature list: operation 3216

AOPs-SVM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0078
application sub category: topic_0154
application sub category: topic 3474
citation: FBIOE.2019.00224
citation: pmcid:PMC6759716
citation: pubmed:31620433
description: A Sequence-Based Classifier of Antioxidant Proteins Using a Support Vector Machine. AOPs-SVM: Sequence-based Classifier of Antioxidant Proteins Using a Support Vector Machine. Input your sequence:(FASTA format)
feature list: operation_0267
feature list: operation_0335
feature list: operation_0418

AOtools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3318
application sub category: topic 3382
citation: OE.27.031316
citation: pubmed:31684366
description: A Python package for adaptive optics modelling and analysis.
feature list: operation 3443
license: LGPL-3.0

AP3
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: acs.analchem.9b02520
citation: pubmed:31247716
description: Proteotypic peptide prediction tool by taking the peptide digestibility into consideration.
feature list: operation_0252
feature list: operation_0418
feature list: operation 2929
is accessible for free: true
license: Unlicense
operating system: Windows
software help: User Guide of AP3.pdf
software version: 1.0
primary contact: Cheng Chang
primary contact: Zhiqiang Gao

APAatlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic 3170
application sub category: topic 3512
citation: gkz876
citation: pmcid:PMC6943053
citation: pubmed:31586392
description: decoding alternative polyadenylation across human tissues. The APA atlas refers to " A lternative P oly A denylation atlas in human tissues". Widespread alternative polyadenylation (APA) occurs during cell proliferation and differentiation, exhibits strong tissue specificity. Recent studies have highlighted the important role of APA in transcription regulation. Here we systematically characterize APA profile in 9,475 samples across 53 human tissues from Genotype-Tissue Expression (GTEx) project with two algorisms, and analyzed the association between APA events with traits and mRNA expression. These APA events may uncover novel mechanisms for the transcription regulation, development of tissues and phenotypes
feature list: operation 2421
feature list: operation 2495
feature list: operation 3196

APEC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0749
application sub category: topic 3173
citation: https://doi.org/10.1101/646331
description: APEC (Accessibility Pattern based Epigenomic Clustering) - single cell epigenomic clustering based on accessibility pattern.
feature list: operation 3192
feature list: operation 3501
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
software help: README.md
primary contact: Bin Li

APHIRM toolkit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3318
application sub category: topic 3416
application sub category: topic 3489
citation: S12891-019-2828-1
citation: pmcid:PMC6822468
citation: pubmed:31666054
description: The APHIRM Toolkit is a set of OHS risk management procedures that target both physical and psychosocial hazards. A participative hazard identification and risk management toolkit for improving the risk management of musculoskeletal disorders.

APIS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2269
application sub category: topic 2885
application sub category: topic 3518
citation: https://doi.org/10.1111/1755-0998.13103
citation: pubmed:31609085
description: An auto-adaptive parentage inference software that tolerates missing parents. Auto-Adaptive Parentage Inference Software Tolerant to Missing Parents. Parentage assignment package. Parentage assignment is performed based on observed average Mendelian transmission probability distributions. The main function of this package is the function APIS(), which is the parentage assignment function
feature list: operation 3196
license: GPL-2.0

APPAGATO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3500
citation: btw223
citation: pubmed:27153658
description: APproximate PArallel and stochastic GrAph querying TOol for biological networks.
feature list: operation_0224
feature list: operation_0495
is accessible for free: true
license: MIT
operating system: Linux
software help: Documentation.pdf
primary contact: Federico Busato
primary contact: Nicola Bombieri

APSiC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 2640
application sub category: topic 3168
citation: https://doi.org/10.1101/807248
description: Systematic Identification of Novel Cancer Genes through Analysis of Deep shRNA Perturbation Screens. APSiC: Analysis of Perturbation Screens for the Identification of Novel Cancer Genes. A web portal using the Shiny framework in R has been developed to visualize rank profiles of the DRIVE shRNA screen and corresponding gene expression data from TCGA at https://apsic.shinyapps.io/APSiC/
feature list: operation 2495
feature list: operation 3435
feature list: operation 3501

AQRNA-seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3170
application sub category: topic 3512
citation: https://doi.org/10.1101/841130
description: Sequencing-based quantitative mapping of the cellular small RNA landscape. Processing scripts for AQ RNA-seq. This repo contains python processing scripts for AQRNA-seq data analysis. The scripts were used in conjuction with open-source tools/algorithms such as fastxtoolkit and blast as described below
feature list: operation 2429
feature list: operation 3192
feature list: operation 3799

AQUA-DUCT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0602
citation: btx125
citation: pubmed:28334160
description: Tool that facilitates analysis of the behaviour of molecules that penetrate any selected region in a protein.
feature list: operation_0387
feature list: operation 2950
feature list: operation 3192
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: apidocs
software help: TIPS AND TRICKS CLUSTERING.pdf
software help: TIPS AND TRICKS TRIMMING.pdf

AQUA-MER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3068
application sub category: topic 3332
application sub category: topic 3489
citation: JCC.26081
citation: pubmed:31603259
description: A database and toolkit for researchers working on environmental mercury geochemistry. AQUA-MER is useful for researchers who want to investigate mercury speciation in defined environments i.e., to which chemical elements and groups it will bind and in what proportions, given an input of concentrations of chemicals.
feature list: operation_0224
feature list: operation 2476

AR-Pred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0176
application sub category: topic_0749
application sub category: topic 3534
citation: prot.25749
citation: pmcid:PMC6718341
citation: pubmed:31141211
description: Active and Regulatory site Prediction (AR‐Pred) to identify protein regulatory and functional binding sites.
feature list: operation 2464
feature list: operation 3896
feature list: operation 3903
is accessible for free: true
license: LGPL-3.0
operating system: Linux
software help: Readme.md
primary contact: Sambit Mishra

ARA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 3382
application sub category: topic 3474
citation: S41598-019-50587-1
citation: pmcid:PMC6778075
citation: pubmed:31586139
description: accurate, reliable and active histopathological image classification framework with Bayesian deep learning. This repository contains an implementation of ARA-CNN - a Bayesian deep learning model intended for histopathological image classification. ARA stands for Accurate, Reliable and Active. Any method that works on patient data needs to be accurate and reliable, meaning that in addition to very high classification accuracy it should also provide a measure of uncertainty for each prediction. ARA-CNN adheres to these requirements. Moreover, the uncertainty measurement can be used as an acquisition function in active learning, which significantly speeds up the learning process on new histopathological datasets. Uncertainty can also be used to identify mislabelled training images
feature list: operation 3283
feature list: operation 3443
feature list: operation 3553
license: MIT

ARDaP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3174
application sub category: topic 3575
application sub category: topic 3673
citation: https://doi.org/10.1101/720607
description: comprehensive antibiotic resistance detection from Burkholderia pseudomallei genomes | Comprehensive resistance detection from WGS data | ARDaP - Antimicrobial Resistance Detection and Prediction | ARDaP was written by Derek Sarovich (@DerekSarovich) (University of the Sunshine Coast, Australia) with database construction, code testing and feature design by Danielle Madden (@dmadden9), Eike Steinig (@EikeSteinig) (Australian Institute of Tropical Health and Medicine, Australia) and Erin Price (@Dr_ErinPrice)
feature list: operation 3196
feature list: operation 3431
feature list: operation 3482

ARGA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0632
application sub category: topic 3168
application sub category: topic 3174
citation: J.ENVINT.2019.04.030
citation: pubmed:31054477
description: Antibiotic Resistance Gene Analyzer.
feature list: operation_0308
feature list: operation 3482
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Ye Deng

ARMOR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 3170
application sub category: topic 3855
citation: G3.119.400185
citation: pmcid:PMC6643886
citation: pubmed:31088905
description: ARMOR (Automated Reproducible MOdular RNA-seq) Workflow for Preprocessing and Differential Analysis of RNA-seq Data.
feature list: operation 2428
feature list: operation 3192
feature list: operation 3800
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: wiki
primary contact: https://orcid.org/0000-0002-3048-5518
primary contact: https://orcid.org/0000-0003-3833-2169

ASA-PS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic 2269
application sub category: topic 3318
application sub category: topic 3421
citation: S12913-019-4640-X
citation: pmcid:PMC6868867
citation: pubmed:31752856
description: Development and validation of a predictive model for American Society of Anesthesiologists Physical Status. BACKGROUND:The American Society of Anesthesiologists Physical Status (ASA-PS) classification system was developed to categorize the fitness of patients before surgery. Increasingly, the ASA-PS has been applied to other uses including justification of inpatient admission. Our objectives were to develop and cross-validate a statistical model for predicting ASA-PS; and 2) assess the concurrent and predictive validity of the model by assessing associations between model-derived ASA-PS, observed ASA-PS, and a diverse set of 30-day outcomes. METHODS:Using the 2014 American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) Participant Use Data File, we developed and internally cross-validated multinomial regression models to predict ASA-PS using preoperative NSQIP data. Accuracy was assessed with C-Statistics and calibration plots
feature list: operation_0337
feature list: operation 2428
feature list: operation 3659

ASA24
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0152
application sub category: topic 3305
application sub category: topic 3390
application sub category: topic 3474
citation: nu11123045
citation: pmcid:PMC6950225
citation: pubmed:31847188
description: The Automated Self-Administered 24-Hour (ASA24) Dietary Assessment Tool is a free web-based tool for collection of automatically coded dietary recalls and/or food records.
feature list: operation 2421
feature list: operation 3359
feature list: operation 3891

ASA3P
type: SoftwareApplication
input: DNA sequence (raw)
  type: FormalParameter
  additional type: data 3497
  encoding format: format 2545
  encoding format: format 2546
  encoding format: format 2572
  encoding format: format 3590
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0622
application sub category: topic 3301
author: http://orcid.org/0000-0003-4216-2721
citation: https://doi.org/10.1101/654319
description: ASA³P is an automatic and highly scalable assembly, annotation and higher-level analyses pipeline for closely related bacterial isolates.
feature list: operation_0323
feature list: operation_0362
feature list: operation_0524
feature list: operation 3216
feature list: operation 3460
feature list: operation 3461
feature list: operation 3482
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: manual.pdf
software version: 1.3.0
primary contact: http://orcid.org/0000-0003-4216-2721

ASD-DiagNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3360
application sub category: topic 3419
application sub category: topic 3444
application sub category: topic 3474
citation: FNINF.2019.00070
citation: pmcid:PMC6890833
citation: pubmed:31827430
description: A Hybrid Learning Approach for Detection of Autism Spectrum Disorder Using fMRI Data. This repository contains the implementation of ASD-DiagNet algorithm
feature list: operation 3359
feature list: operation 3799
license: GPL-3.0

ASHLAR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
additional type: Web application
application sub category: topic_0749
application sub category: topic 1317
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3382
application sub category: topic 3400
application sub category: topic 3500
citation: s41597-019-0332-y
citation: btac544
citation: pmcid:PMC6917801
citation: pmcid:PMC9525007
citation: pubmed:31848351
citation: pubmed:35972352
description: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration. Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer.
feature list: operation_0337
feature list: operation 3435
feature list: operation 3443
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: installation.html

ASJA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3512
citation: J.CSBJ.2019.08.001
citation: pmcid:PMC6709372
citation: pubmed:31462970
description: A Program for Assembling Splice Junctions Analysis | RNA splicing may generate different kinds of splice junctions, such as linear, back-splice and fusion junctions. Only a limited number of programs are available for detection and quantification of splice junctions. Here, we present Assembling Splice Junctions Analysis (ASJA), a software package that identifies and characterizes all splice junctions from high-throughput RNA sequencing (RNA-seq) data. ASJA processes assembled transcripts and chimeric alignments from the STAR aligner and S tringTie assembler. ASJA provides the unique position and normalized expression level of each junction. Annotations and integrative analysis of the junctions enable additional filtering. It is also appropriate for the identification of novel junctions. Implementation and Dependencies
feature list: operation_0232
feature list: operation_0264
feature list: operation 3800

ASM-Clust
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0610
application sub category: topic_0623
application sub category: topic_0637
application sub category: topic 3300
citation: https://doi.org/10.1101/792739
description: classifying functionally diverse protein families using alignment score matrices. the three scripts in this directory comprise ASM-clust, an approach to de novo classify complex protein superfamilies ASM-clust is intended to. ASM-Clust is implemented in bash with two helper scripts in perl, and will take a protein fasta file as the sole input. Fasta files are processed with ASM_clust.sh, which then:
feature list: operation_0291
feature list: operation 3644

ASNR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0602
application sub category: topic_0610
application sub category: topic 3500
citation: S41597-019-0056-Z
citation: pmcid:PMC6488576
citation: pubmed:31036810
description: Animal Social Networks Repository - repository of interaction data from published studies of wild, captive, and domesticated animals.
feature list: operation 3562
feature list: operation 3766
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Shweta Bansal

ASRD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0625
application sub category: topic_0659
application sub category: topic_0780
application sub category: topic 3168
application sub category: topic 3512
citation: PP.19.00959
citation: pubmed:31843802
description: An online database for exploring over 2,000 Arabidopsis small RNA libraries.
feature list: operation_0224
feature list: operation 3196
feature list: operation 3435

ATBdiscrimination
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0820
application sub category: topic 3324
application sub category: topic 3384
citation: ACS.JCIM.9B00678
citation: pubmed:31609612
description: An in Silico Tool for Identification of Active Tuberculosis Disease Based on Routine Blood Test and T-SPOT.TB Detection Results. Welcome to ATB assistant discrimination!. Home Document Datasets Contact Us. Approximately one third of the world's population is infection with Mycobacterium tuberculosis. They are at a high risk progression to active tuberculosis (ATB) during their lifetime, so it is urgent and vital to develop diagnostic methods that can distinguish ATB from latent tuberculosis infection. Please input single sample data in the text form:. Please Cite: Jiangpeng Wu, Jun Bai, Wei Wang, Lili Xi, Pengyi Zhang, Jingfeng Lan, Liansheng Zhang*, Shuyan Li*. ATBdiscrimination: An in Silico Tool for Identification of Active Tuberculosis Disease Based on Routine Blood Test and T-SPOT.TB Detection Results. J. Chem. Inf. Model., 2019, doi: 10.1021/acs.jcim.9b00678

ATC-NLSP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0202
application sub category: topic_0209
application sub category: topic 3474
citation: FPHAR.2019.00971
citation: pmcid:PMC6739564
citation: pubmed:31543820
description: Prediction of the Classes of Anatomical Therapeutic Chemicals Using a Network-Based Label Space Partition Method | codes for the drug class prediction paper | Codes and dataset for "Network-based label space partition for predicting the classes of anatomical therapeutic chemicals"
feature list: operation 3502
license: GPL-3.0

ATEN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3474
citation: BTZ563
citation: pubmed:31368481
description: And/Or Tree Ensemble for inferring accurate Boolean network topology and dynamics | # Download the development version of ATEN from GitHub: | Note: please note that set.seed() is not suitable for the Package parallel. In order to make the results reproducible, we introduced function clusterSetRNGStream(), more deatails please see the Pacakge parallel | B, the number of And/Or trees in ATEN. This parameter always depends on the size/noise of the data. We suggest you set a higher B for large/noisy networks. If you set a very large B, although it won't affect the results much, but it takes much time..
feature list: operation_0277
feature list: operation 3439
feature list: operation 3562
license: GPL-2.0

AUPA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3421
application sub category: topic 3474
citation: S11517-019-02036-4
citation: pubmed:31468306
description: Design a prototype for automated patient diagnosis in wireless sensor networks | It is indeed necessary to design of an elderly support mobile healthcare and monitoring system on wireless sensor network (WSN) for dynamic monitoring. It comes from the need for maintenance of healthcare among patients and elderly people that leads to the demand on change in traditional monitoring approaches among chronic disease patients and alert on acute events. In this paper, we propose a new automated patient diagnosis called automated patient diagnosis (AUPA) using ATmega microcontrollers over environmental sensors. AUPA monitors and aggregates data from patients through network connected over web server and mobile network. The scheme supports variable data management and route establishment. Data transfer is established using adaptive route discovery and management approaches

AUTALASSO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3517
application sub category: topic 3810
citation: s12859-019-2743-3
citation: pmcid:PMC6444607
citation: pubmed:30940067
description: Automatic adaptive LASSO for genome-wide prediction.
feature list: operation 3196
feature list: operation 3557
feature list: operation 3659
is accessible for free: true
operating system: Linux
operating system: Mac
primary contact: Patrik Waldmann

AVADA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0218
application sub category: topic 3474
citation: S41436-019-0643-6
citation: pmcid:PMC7301356
citation: pubmed:31467448
description: Toward automated pathogenic variant evidence retrieval directly from the full-text literature | PURPOSE:Both monogenic pathogenic variant cataloging and clinical patient diagnosis start with variant-level evidence retrieval followed by expert evidence integration in search of diagnostic variants and genes. Here, we try to accelerate pathogenic variant evidence retrieval by an automatic approach. METHODS:Automatic VAriant evidence DAtabase (AVADA) is a novel machine learning tool that uses natural language processing to automatically identify pathogenic genetic variant evidence in full-text primary literature about monogenic disease and convert it to genomic coordinates. RESULTS:AVADA automatically retrieved almost 60% of likely disease-causing variants deposited in the Human Gene Mutation Database (HGMD), a 4.4-fold improvement over the current best open source automated variant extractor
feature list: operation 2422
feature list: operation 3227
feature list: operation 3431

AVA,Dx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3512
application sub category: topic 3676
citation: S13073-019-0670-6
citation: pmcid:PMC6767648
citation: pubmed:31564248
description: Identifying Crohn's disease signal from variome analysis | prediction of individual predisposition to disease x through variation analysis | After years of concentrated research efforts, the exact cause of Crohn’s disease (CD) remains unknown
feature list: operation_0487
feature list: operation 3196
feature list: operation 3501

AbLIFT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0130
application sub category: topic_0199
application sub category: topic 2830
citation: JOURNAL.PCBI.1007207
citation: pmcid:PMC6728052
citation: pubmed:31442220
description: An web application that designs multipoint core mutations to improve contacts between specific Fv light and heavy chains.
feature list: operation 3202
feature list: operation 3216

AcCNET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0121
application sub category: topic_0602
citation: btw601
citation: pubmed:27663497
description: AcCNET (Accessory genome Constellation Network) - application that aims to compare accessory genomes of a large number of genomic units, both at qualitative and quantitative levels.
feature list: operation_0362
feature list: operation 2495
feature list: operation 3192
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.txt
primary contact: Val F. Lanza

AcRanker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0798
application sub category: topic 3474
application sub category: topic 3810
citation: https://doi.org/10.1101/854950
description: AcRanker is a machine learning system developed in python that ranks proteins in a proteome as per their Anti-CRISPR tendencies predicted using sequence features.
feature list: operation_0253
feature list: operation 3092
feature list: operation 3096

AcetoBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0602
application sub category: topic_0632
application sub category: topic_0821
application sub category: topic 3168
application sub category: topic 3174
citation: BAZ142
citation: pmcid:PMC6908459
citation: pubmed:31832668
description: AcetoBase is a dedicated repository and curated database for the analysis of acetogenic bacteria based on the key functional gene formyltetrahydrofolate synthetase (FTHFS/fhs) of Wood-Ljungdahl Pathway for Acetogenesis.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3460

ActiveDriver
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0622
application sub category: topic 2269
application sub category: topic 2640
application sub category: topic 3175
citation: msb.2012.68
citation: pmcid:PMC3564258
citation: pubmed:23340843
description: ActiveDriver is a computational method for identifying post-translational modification (PTM) sites (i.e., active sites) in proteins that are significantly mutated in cancer genomes. ActiveDriver provides signalling-related interpretation of single nucleotide variants (SNVs) identified in cancer genome sequencing.
feature list: operation 2415
feature list: operation 2454
feature list: operation 3197
feature list: operation 3225
feature list: operation 3504
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: activedriver
software help: ActiveDriver.pdf
software version: 1.0.0
primary contact: https://orcid.org/0000-0002-2299-2309

AdTree
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0610
application sub category: topic 3315
citation: PREPRINTS201907.0058.V2
description: Accurate, Detailed, and Automatic Modelling of Laser-Scanned Trees | AdTree implements the tree reconstruction method described in the following paper: | 3D Trees reconstructed from point clouds
feature list: operation 3478
feature list: operation 3891
license: GPL-3.0

AdaReg
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2269
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/869362
description: An R package for data Adaptive Robust Estimation in Linear Regression with Application in GTEx Gene Expressions.
feature list: operation 3196
feature list: operation 3435
feature list: operation 3659
license: GPL-3.0

AdditiveChem
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 2840
application sub category: topic 3407
citation: J.FOODCHEM.2019.125519
citation: pubmed:31648087
description: A comprehensive bioinformatics knowledge-base for food additive chemicals. A comprehensive food additive database. Supported search options:Text query, Structure, Fragment, Similarity, MCS. Food additives are considered to be the catalysts and headstones of the modern food industry, affecting every step of food production, processing, and storage. Fields searchable in this way are:CAS number,JECFA number,FEMA number,CoE number,Name,InChI,InChI key,INS
feature list: operation 2421

AdequacyModel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 3474
citation: JOURNAL.PONE.0221487
citation: pmcid:PMC6710032
citation: pubmed:31450236
description: An R package for probability distributions and general purpose optimization | Several lifetime distributions have played an important role to fit survival data. However, for some of these models, the computation of maximum likelihood estimators is quite difficult due to presence of flat regions in the search space, among other factors. Several well-known derivative-based optimization tools are unsuitable for obtaining such estimates. To circumvent this problem, we introduce the AdequacyModel computational library version 2.0.0 for the R statistical environment with two major contributions: a general optimization technique based on the Particle Swarm Optimization (PSO) method (with a minor modification of the original algorithm) and a set of statistical measures for assessment of the adequacy of the fitted model

Adjutant
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3068
citation: bty722
citation: pubmed:30875428
description: R-based tool to support topic discovery for systematic and literature reviews.
feature list: operation_0306
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Anamaria Crisan

Adult Fruitfly Brain Atlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3304
description: A Web resource enabling to inspect the neuroanatomy of the fruit fly, equipped with a graphical interface enabling users to color structures on brain sections.

Afann
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic 3168
application sub category: topic 3474
citation: S13059-019-1872-3
citation: pmcid:PMC6891986
citation: pubmed:31801606
description: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression. Alignment-Free methods Adjusted by Neural Network. Afann (Alignment-Free methods Adjusted by Neural Network) is an alignment-free software that supports fast calculation of different dissimilarity measures including d2star, d2shepp, CVtree, Manhattan, Euclidean and d2. It also adjusts the bias of d2star and d2shepp calculated from sequencing samples
feature list: operation 3435
feature list: operation 3472
feature list: operation 3659

AfumID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3305
citation: MBIO.00392-19
citation: pmcid:PMC6529631
citation: pubmed:31113894
description: framework for the analysis of Aspergillus fumigatus isolates based on their microsatellite profile.
feature list: operation 3196
feature list: operation 3797
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-7239-4817

AggreRATE-Pred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0634
application sub category: topic 3292
application sub category: topic 3315
application sub category: topic 3368
citation: BTZ764
citation: pubmed:31599925
description: A mathematical model for the prediction of change in aggregation rate upon point mutation. Protein aggregation is a major unsolved problem in biochemistry with implications for several human diseases (including type II diabetes, corneal dystrophy and most of neurodegenerative disease like Alzheimer's disease, Parkinson's disease, huntington's disease etc.) as well as for biotechnology and bio-material science products (such as human recombinant proteins, monoclonal antibodies, industral enzymes and vaccines). AggreRATE-Pred is a linear regression based tool which can predict the change in aggregation rate upon point mutation for the given protein
feature list: operation_0331
feature list: operation 2426
feature list: operation 3436
feature list: operation 3659

Aggrescan3D
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0123
application sub category: topic_0130
application sub category: topic_0199
citation: btz143
citation: pubmed:30825368
description: Package for structure-based prediction of protein aggregation properties and rational design of protein solubility.
feature list: operation_0244
feature list: operation_0409
feature list: operation 3436
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: master
software help: Home
primary contact: Michal Jamroz
primary contact: Rafael Zambran

AgroLD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3810
description: The RDF Knowledge-based Database for plant molecular networks.

AgroPortal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic 3810
description: Browser for ontologies for agricultural science based on NBCO BioPortal.

Alevin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 3170
application sub category: topic 3512
citation: s13059-019-1670-y
citation: pmcid:PMC6437997
citation: pubmed:30917859
description: Tool introducing a family of algorithms for quantification and analysis of 3’ tagged-end single-cell sequencing data.
feature list: operation 2495
feature list: operation 3200
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: alevin.html
primary contact: A. Srivastava
primary contact: Rob Patro

AliTV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0081
application sub category: topic_0622
application sub category: topic 3293
application sub category: topic 3500
citation: PEERJ.PREPRINTS.2348V2
description: AliTV-interactive visualization of whole genome comparisons. Visualize whole genome alignments as linear maps. For the perl part, see AliTV-perl-interface. You do not need to install anything to try the interactive visualization of AliTV. Just navigate to the demo page to try all the features on an example dataset (seven chloroplast genomes). You can also import your own json files on that page. When loading your own data into AliTV it is not transferred to a server but remains on your local machine. Read the documentation at readthedocs
feature list: operation_0337
feature list: operation 3182
feature list: operation 3198
feature list: operation 3209
license: MIT

All-FIT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3360
citation: btz865
citation: https://doi.org/10.1101/625376
citation: pmcid:PMC7141867
citation: pubmed:31750888
description: Allele-Frequency-based Imputation of Tumor Purity from High-Depth Sequencing Data.
feature list: operation 3227
feature list: operation 3557
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Khiabanian Lab

AlleleAnalyzer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic 3421
application sub category: topic 3912
citation: S13059-019-1783-3
citation: pmcid:PMC6694686
citation: pubmed:31416467
description: a tool for personalized and allele-specific sgRNA design | A software tool for personalized and allele-specific CRISPR editing | The CRISPR/Cas system is a highly specific genome editing tool capable of distinguishing alleles differing by even a single base pair. Target sites might carry genetic variations that are not distinguishable by sgRNA designing tools based on one reference genome. AlleleAnalyzer is open-source software that incorporates single nucleotide variants and short insertions and deletions to design sgRNAs for precisely editing one or multiple haplotypes of a sequenced genome, currently supporting eleven Cas proteins. It also leverages patterns of shared genetic variation to optimize sgRNA design for different human populations. AlleleAnalyzer is available at https://github.com/keoughkath/AlleleAnalyzer
feature list: operation_0487
feature list: operation 3096
feature list: operation 3197
license: MIT

AlloDriver
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0199
application sub category: topic 2640
citation: GKZ350
citation: pmcid:PMC6602569
citation: pubmed:31069394
description: Method for the identification and analysis of cancer driver targets.
feature list: operation_0331
feature list: operation 3227
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.jsp#
primary contact: 0000-0002-6558-791X

AlphaBeta
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0199
application sub category: topic_0654
application sub category: topic_0780
application sub category: topic 3295
citation: s13059-020-02161-6
citation: pmcid:PMC7539454
citation: pubmed:33023650
description: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to: 1. analyze 'germline' epimutations in the context of multi-generational mutation accumulation lines (MA-lines). 2. analyze 'somatic' epimutations in the context of plant development and aging
feature list: operation 3196
feature list: operation 3204
feature list: operation 3799
license: GPL-3.0

AlphaFamImpute
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3518
citation: btaa499
citation: pmcid:PMC7520044
citation: pubmed:32467963
description: AlphaFamImpute is a genotype calling, phasing, and imputation algorithm for large full-sib families in diploid plants and animals which supports individuals genotyped with SNP array or GBS data.
feature list: operation_0484
feature list: operation_0487
feature list: operation 3196
feature list: operation 3454
feature list: operation 3557

AlphaSeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 3382
application sub category: topic 3474
citation: TNNLS.2019.2942951
citation: pubmed:31634848
description: A method for sequence discovery with deep reinforcement learning.
feature list: operation 3695

AluMine
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3673
citation: s13100-019-0174-3
citation: pmcid:PMC6639938
citation: pubmed:31360240
description: > CORRECT NAME OF TOOL COULD ALSO BE 'Conclusions:AluMine' | alignment-free method for the discovery of polymorphic Alu element insertions | Scripts for discovery and genotyping polymorphic Alu element insertions in human genomes | git clone https://github.com/bioinfo-ut/AluMine | This GitHub repository stores various scripts required to discover and genotype polymorphic Alu element insertions. There are four different workflows: REF-plus discovery, REF-minus discovery, merging and filtering workflow and genotyping workflow. REF-plus and REF-minus workflows generate text file containing 32-mer pairs that can be subsequently used for genotyping using FastGT package. The scripts are written in PERL and bash | Please cite: Puurand T, Kukuškina V, Pajuste F-D, Remm M. (2019). AluMine: alignment-free method for the discovery of polymorphic Alu element insertions. Mobile DNA 10:31. [https://doi.org/10.1186/s13100-019-0174-3](doi: https://doi.org/10.1186/s13100-019-0174-3)
feature list: operation_0308
feature list: operation_0484
feature list: operation 3196
license: GPL-3.0
provider: https://orcid.org/0000-0003-3966-8422

AluScanCNV2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2640
application sub category: topic 3168
application sub category: topic 3474
citation: j.gendis.2018.09.001
citation: pmcid:PMC6411622
citation: pubmed:30906832
description: R package for copy number variation calling and cancer risk prediction with next-generation sequencing data.
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Taobo Hu

AlvisIR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0218
application sub category: topic 3050
application sub category: topic 3301
citation: j.fm.2018.04.011
citation: pmcid:PMC6460834
citation: pubmed:30910089
description: Text mining tool for extracting information about microbial biodiversity in food.
feature list: operation_0224
feature list: operation_0306
feature list: operation 3798
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: https://github.com/Bibliome/alvisir/wiki/How-to-use-Alvis-Search-Engine%3F
primary contact: Robert Bossy

Alyx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3365
application sub category: topic 3489
citation: https://doi.org/10.1101/827873
description: Data architecture and visualization for a large-scale neuroscience collaboration. Database for experimental neuroscience laboratories. Documentation: http://alyx.readthedocs.io. The setup.py script sets up postgres (it creates the database and postgres user), it sets up the alyx/alyx/settings_secret.py file with the postgres database connection information, it creates the Python virtual environment with the dependencies (including django), and it creates all the required SQL tables. Note that the postgres username and password are distinct from Alyx (Django) users and password. There is only one postgres user that is only used locally for maintenance task or by Django
feature list: operation_0337
feature list: operation 2421
feature list: operation 2422
software help: latest

AmpliSolve
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 3168
application sub category: topic 3342
citation: S12920-019-0557-9
citation: pmcid:PMC6679440
citation: pubmed:31375105
description: Identification of single nucleotide variants using position-specific error estimation in deep sequencing data | Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling
feature list: operation 3192
feature list: operation 3196
feature list: operation 3227

AmpliconTagger
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0659
application sub category: topic_0769
application sub category: topic 3168
application sub category: topic 3174
application sub category: topic 3316
citation: GIZ146
citation: pmcid:PMC6901069
citation: pubmed:31816087
description: Systematic processing of ribosomal RNA gene amplicon sequencing data. This is the AmpliconTagger home page. AmpliconTagger pipeline - for various types of amplicon sequencing data. By Julien Tremblay - julien.tremblay_at_nrc-cnrc.gc.ca
feature list: operation 3192
feature list: operation 3218
feature list: operation 3460

AmtDB
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 2330
output: Sequence features
  type: FormalParameter
  additional type: data 1255
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0622
author: 0000-0003-1338-638X
citation: gky843
citation: pmcid:PMC6324066
citation: pubmed:30247677
description: This is the place where you can find an updated list of the published mitochondrial sequences coming from the ancient DNA samples (aDNA). The main interest of our database lies in the anatomically modern Homo sapiens samples, ranging from the late Paleolithic to roughly Iron Age times, focusing on an Euroasian geographical area. We provide both the mtDNA sequences (in FASTA format), and the metadata for the samples (IDs, dates, geolocation, site, culture, mtDNA haplogroup etc., available to download in a tab-delimited text file).
feature list: operation_0226
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
provider: Institute of Molecular Genetics AS CR
software help: div-tab-docs
software version: v1.007
primary contact: https://orcid.org/0000-0003-1774-0091
primary contact: https://orcid.org/0000-0003-3059-6127

AmyCo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3337
application sub category: topic 3407
citation: https://doi.org/10.1080/13506129.2019.1603143
citation: pubmed:31094220
description: Collection of amyloidoses and other clinical disorders related to amyloid deposition.
feature list: operation 3431
feature list: operation 3436
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: manual

Anabel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0821
application sub category: topic 3068
application sub category: topic 3489
citation: BAZ101
citation: pmcid:PMC6790968
citation: pubmed:31608948
description: A software designed for the analysis of binding curves with which to evaluate the interactions of biomolecules.
feature list: operation_0224
feature list: operation_0306
feature list: operation 3778
license: MIT

AnalyzER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0611
application sub category: topic_0780
application sub category: topic 3452
citation: s41467-019-08893-9
citation: pmcid:PMC6395764
citation: pubmed:30816109
description: Software package for quantitative analysis of plant ER architecture and dynamics.
feature list: operation 3216
feature list: operation 3435
feature list: operation 3799
is accessible for free: true
operating system: Windows
software help: er-network-analysis
software help: analyzer v1.1.pdf
software version: 1.1
primary contact: Dr M.D. Fricker

Anchor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3168
application sub category: topic 3173
citation: gr.237156.118
citation: pmcid:PMC6360811
citation: pubmed:30567711
description: Package for trans-cell type prediction of transcription factor binding sites.
feature list: operation_0417
feature list: operation_0445
feature list: operation 2575
is accessible for free: true
operating system: Linux
operating system: Mac
software help: README.md

Anchored Multiplier Calculator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2269
application sub category: topic 3305
citation: dyz101
citation: pmcid:PMC6929553
citation: pubmed:31106350
description: Estimating the number of people in hidden populations is needed for public health research, yet available methods produce highly variable and uncertain results. The Anchored Multiplier calculator uses a Bayesian framework to synthesize multiple population size estimates to generate a consensus estimate.
feature list: operation 3658
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: anchored-multiplier-instructions-2019.pdf
primary contact: Paul D. Wesson

Aneuvis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0654
application sub category: topic 3673
citation: s12859-019-2842-1
citation: pmcid:PMC6580570
citation: pubmed:31208319
description: Web-based exploration of numerical chromosomal variation in single cells.
feature list: operation 1812
feature list: operation 3233
feature list: operation 3799
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: aneuvis
primary contact: Daniel Pique

Animal-ImputeDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3500
application sub category: topic 3518
application sub category: topic 3673
citation: gkz854
citation: pmcid:PMC6943029
citation: pubmed:31584087
description: A comprehensive database with multiple animal reference panels for genotype imputation.
feature list: operation_0484
feature list: operation_0487
feature list: operation 3196
feature list: operation 3557
feature list: operation 3661

Anncolvar
type: SoftwareApplication
input: Trajectory data
  type: FormalParameter
  additional type: data 3870
  encoding format: format 3867
output: Molecular property
  type: FormalParameter
  additional type: data 2087
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3892
citation: fmolb.2019.00025
citation: pmcid:PMC6482212
citation: pubmed:31058167
description: Anncolvar builds a feed-forward neural network for approximation of a collective variable of a molecular system. Molecular simulations are slow due to fact that a studied system tends to stay in local energy minima. Methods such as metadynamics address this problem by application of artificial forces acting on collective variables. Collective variables are some descriptors of the state of the molecular system. For example, when simulation binding of a ligand to protein it is possible to use their distance as a collective variable and by applying force onto this collective variable you can accelerate binding and unbinding. However, some sophisticated collective variables are difficult to calculate. For this purpose we developed Anncolvar to approximate such collective variables using artificial neural network.
feature list: operation 2476
is accessible for free: true
license: MIT
operating system: Linux
software help: README.rst
software help: https://github.com/spiwokv/anncolvar/tree/master/docs/html
software version: v0.2
software version: v0.3
software version: v0.4
software version: v0.5
software version: v0.6
primary contact: Vojtech Spiwok

AnnoTree
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0084
application sub category: topic_0194
application sub category: topic_0821
citation: GKZ246
citation: pmcid:PMC6511854
citation: pubmed:31081040
description: Interactive, functionally annotated bacterial tree of life that integrates taxonomic, phylogenetic and functional annotation data.
feature list: operation_0558
feature list: operation_0567
feature list: operation 3478
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: annotree-docs.readthedocs.io

Annot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0121
application sub category: topic_0203
application sub category: topic_0219
application sub category: topic 3518
citation: S12859-019-3147-0
citation: pmcid:PMC6824123
citation: pubmed:31675914
description: a Django-based sample, reagent, and experiment metadata tracking system. Annot and information about what Annot is can be found here: https://gitlab.com/biotransistor/annot . This here is just tutorial material for the tutorial described here: http://annot.readthedocs.io/en/latest/man_tutorial.html . Welcome to Annotamentum’s Documentation. — Annot 5 documentation. Welcome to Annotamentum’s Documentation.¶. Django admin based sample, reagent and experiment metadata tracking. Summary: Annot is a web application, developed for biological wetlab experiment layout, sample and reagent logging, so that data is ready for sharing and analysis. On its core annot makes use of the acpipe_anjson library and acjson - assay coordinate json - file format. The use of controlled vocabulary from ontologies for sample and reagent annotation is enforced. Annot’s modular implementation can be adapted to a variety of experimental paradigms
feature list: operation_0361
feature list: operation_0558
feature list: operation 2422
feature list: operation 3553
software help: latest
software help: annotTutorial

AnnotSV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0091
application sub category: topic_0199
application sub category: topic 3053
application sub category: topic 3168
application sub category: topic 3175
citation: bty304
citation: gkab402
citation: pmcid:PMC8262758
citation: pubmed:29669011
citation: pubmed:34023905
description: Integrated tool for annotation and ranking of structural variations.
feature list: operation_0226
feature list: operation 3197
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: README.AnnotSV latest.pdf
software help: faq
primary contact: https://orcid.org/0000-0002-4149-0857

AnomiGAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0622
application sub category: topic 3315
application sub category: topic 3474
citation: pubmed:31797628
description: Generative Adversarial Networks for Anonymizing Private Medical Data. Scikit-learn library package (version 0.18). Keras library package (version 2.0.6)
feature list: operation 3283

AnthOligo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0632
application sub category: topic 3168
citation: btaa552
description: Automating the design of oligonucleotides for capture/enrichment technologies. AnthOligo is a web-based application developed to automatically generate oligo sequences to be used for the targeting and capturing the continuum of large and complex genomic regions. It automates the complex process of checking multiple applications so that the oligos selected successfully pass certain specific parameter criteria and then get shortlisted as a possible use case for RSE (region specific extraction) processes
feature list: operation_0308
feature list: operation_0309
feature list: operation_0335

AntiBac-Pred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic_0209
application sub category: topic_0821
application sub category: topic 3303
citation: ACS.JCIM.9B00436
citation: pubmed:31661960
description: A Web Application for Predicting Antibacterial Activity of Chemical Compounds. Predict Targets for Drawn Structure. Discovery of novel antibacterial agents is the high-priority task because the existing therapy do not provide the necessary safety and sufficient long-term efficacy due to the emerging resistance [1]. The process may be optimized using (Q)SAR methods based on the accumulated experimental data in the field. Nowadays, data on antibacterial action of chemical compounds are well represented in public domain. ChEMBL database [2], for example, contains records on activity of chemical compounds against 1386 bacteria. We extracted bioactivity records on minimum inhibitory concentrations (MICs) of chemical compounds from ChEMBL_24 and prepared them as follows:. antiBac-Pred allows user to predict the fact that chemical compound can inhibit the growth of one or more of 353 bacteria in concentration below the 10000 nM
feature list: operation_0417
feature list: operation 3860

AntiHIV-Pred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3047
application sub category: topic 3336
citation: btz638
citation: pmcid:PMC7523681
citation: pubmed:31418763
description: Web-resource for in silico prediction of anti-HIV/AIDS activity | MOTIVATION:Identification of new molecules promising for treatment of HIV-infection and HIV-associated disorders remains an important task in order to provide safer and more effective therapies. Utilization of prior knowledge by application of computer-aided drug discovery approaches reduces time & financial expenses and increases the chances of positive results in anti-HIV R&D. To provide the scientific community with a tool that allows estimating of potential agents for treatment of HIV-infection and its comorbidities, we have created a freely-available web-resource for prediction of relevant biological activities based on the structural formulae of drug-like molecules

ApicoTFdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0623
application sub category: topic_0749
citation: BAZ094
citation: pmcid:PMC6748703
citation: pubmed:31529106
description: The comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors | Despite significant progress in apicomplexan genome sequencing and genomics, the current list of experimentally validated transcription factors (TFs) in these genomes is incomplete and mainly consists of AP2 family of proteins, with only a limited number of non-AP2 family TFs and transcription-associated co-factors (TcoFs). We have performed a systematic bioinformatics-aided prediction of TFs and TcoFs in apicomplexan genomes and developed the ApicoTFdb database which consists of experimentally validated as well as computationally predicted TFs and TcoFs in 14 apicomplexan species. The predicted TFs are manually curated to complement the existing annotations. The current version of the database includes 1292 TFs which includes experimentally validated and computationally predicted TFs, representing 20 distinct families across 14 apicomplexan species
feature list: operation 2492

AppA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0130
application sub category: topic 2830
application sub category: topic 3297
citation: GKZ358
citation: pmcid:PMC6602511
citation: pubmed:31069385
description: Web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody-antigen structures and models.
feature list: operation_0272
feature list: operation_0394
feature list: operation 2950
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help appa.html
primary contact: Chandra S Verma
primary contact: Minh N Nguyen
primary contact: Pingyu Zhong

AppleMDO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3169
application sub category: topic 3170
application sub category: topic 3173
citation: FPLS.2019.01333
citation: pmcid:PMC6817610
citation: pubmed:31695717
description: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. AppleMDO is a multi-dimensional omics database. Users can submit locus IDs to quickly search for co-expression networks, functional modules, chromatin states and enriched epigenetic marks. For gene lists in search results, gene expression profiling analysis and functional enrichment analysis tools are provided to systematically extract biological themes from gene lists. Additionally, the basic structural and functional annotations of each gene can be obtained, such as gene families, KEGG annotations, GO terms, orthologues in thirteen species and Pfam domains. In addition, some functional support toolkits are also provided, such as GO analysis, blast, motif analysis, ID conversion, sequence extraction and the UCSC genome browser. We hope that AppleMDO will benefit apple research communities and serve as a reference for other fruit trees
feature list: operation 2436
feature list: operation 3439
feature list: operation 3672

Aquila_stLFR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic 2885
application sub category: topic 3673
citation: https://doi.org/10.1101/742239
description: Assembly based variant calling package for stLFR and hybrid assembly for linked-reads | Human haplotype-resolved assembly and variant detection for stLFR, hybrid assembly for linked-reads | Install through Bioconda (The updated version 1.2.11): | Aquila_stLFR_assembly_based_variants_call --help | (Please ensure channels are properly setup for bioconda before installing) | Aquila_stLFR utilizes Python3 (+ numpy, pysam, and scipy), SAMtools, and minimap2. To be able to execute the above programs by typing their name on the command line, the program executables must be in one of the directories listed in the PATH environment variable (".bashrc")
feature list: operation_0487
feature list: operation_0525
feature list: operation 3227

Arabidopsis Interactions Viewer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic 3557
citation: pp.18.01216
citation: pmcid:PMC6446796
citation: pubmed:30679268
description: Proteome-wide structure-based prediction of protein-protein interactions in Arabidopsis.
feature list: operation_0478
feature list: operation 2497
feature list: operation 2949
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Nicholas Provart

Arriba
type: SoftwareApplication
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1931
  encoding format: format 2572
  encoding format: format 2573
  encoding format: format 3462
output: Sequence variations
  type: FormalParameter
  additional type: data 3498
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3175
application sub category: topic 3320
application sub category: topic 3512
description: Arriba is a command-line tool to detect gene fusions from RNA-Seq data based on the STAR aligner. In addition to fusions, it can detect exon duplications/inversions and truncations of genes (i.e., breakpoints in introns and intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge.
feature list: operation 3199
feature list: operation 3228
is accessible for free: true
license: MIT
operating system: Linux
software help: arriba.readthedocs.io

ArrowSAM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3673
application sub category: topic 3676
citation: ICCAIS48893.2020.9096725
citation: s12864-020-07013-y
citation: pmcid:PMC7677819
citation: pubmed:33208101
description: ArrowSAM is an in-memory Sequence Alignment/Map (SAM) representation which uses Apache Arrow framework (A cross-language development platform for in-memory data) and Plasma (Shared-Memory) Object Store to store and process SAM columnar data in-memory.
feature list: operation 2409
feature list: operation 3182

Arteria
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0769
application sub category: topic 3068
application sub category: topic 3673
citation: GIZ135
citation: pmcid:PMC6905352
citation: pubmed:31825479
description: An automation system for a sequencing core facility. StackStorm packs to automate sequencing center operations. Event-driven sequencing center automation. It forms the core of the Arteria automation system, which you can read about on our website or preprint. This pack integrates with a series of bioinformatic micro-services, which can be found at https://github.com/arteria-project. This pack provides re-usable units for automating tasks at a sequencing core facility using the StackStorm event-driven automation platform. Handling sequencing data from massive parallel sequencing can be a daunting task! And while the process of handling sequencing data will share many of its characteristics across centers, the current norm is one center one solution. This creates a situation where reuse is difficult to achieve and the wheel is invented over and over again. This is a situation that we hope can be remedied in the form of the Arteria project
feature list: operation 1812
feature list: operation 3431
feature list: operation 3436
license: MIT

ArtiFuse
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: BTZ613
citation: pubmed:31373612
description: Computational validation of fusion gene detection tools without relying on simulated reads | MOTIVATION:Gene fusions are an important class of transcriptional variants that can influence cancer development and can be predicted from RNA sequencing (RNA-seq) data by multiple existing tools. However, real world performance of these tools is unclear due to the lack of known positive and negative events, especially with regard to fusion genes in individual samples. Often simulated reads are used, but these cannot account for all technical biases in RNA-seq data generated from real samples. RESULTS:Here we present ArtiFuse, a novel approach that simulates fusion genes by sequence modification to the genomic reference, and therefore can be applied to any RNA-seq dataset without the need for any simulated reads

AsANet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0780
citation: s11103-016-0469-4
citation: pubmed:27007138
description: A complete network for ascorbic acid (including associated pathways) with a list of the identified genetic variants in tomato genome through a methodology that integrates gene annotations and transcriptome. It represents the only available collection, exhaustive and detailed, on ascorbic acid network in tomato.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1

AsCRISPR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2885
application sub category: topic 3399
application sub category: topic 3577
citation: https://doi.org/10.1101/672634
description: a web server for allele-specific sgRNA design in precision medicine | Abstract Allele-specific targeting by CRISPR provides a point of entry for personalized gene therapy of dominantly inherited diseases, by selectively disrupting the mutant alleles or disease-causing single nucleotide polymorphisms (SNPs), ideally while leaving normal alleles intact. Despite unprecedented specificity and tremendous therapeutic utility of allele-specific targeting by CRISPR, few bioinformatic tools have been implemented for the allele-specific purpose. We thus developed AsCRISPR ( A llele- s pecific CRISPR ), a web tool to aid the design of guide sequences that can discriminate between alleles. It can process with query sequences harboring single-base or short insertion-deletion (indel) mutations, as well as heterozygous SNPs deposited in the dbSNP database. Multiple CRISPR nucleases and their engineered variants including newly-developed Cas12b and CasX are included for users’ choice
feature list: operation 3096
feature list: operation 3431

AspWood
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0152
application sub category: topic_0780
application sub category: topic 3172
citation: tpj.14417
citation: pmcid:PMC6852159
citation: pubmed:31111606
description: Whole-genome annotation and functional analyses based on RNA expression data.
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Ewa Mellerowicz

Assemblytics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 3673
citation: btw369
citation: pmcid:PMC6191160
citation: pubmed:27318204
description: Web analytics tool for the detection of variants from an assembly.
feature list: operation_0525
feature list: operation 3216
feature list: operation 3227
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Maria Nattestad

AssessORF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
citation: btz714
citation: pmcid:PMC7998711
citation: pubmed:31532487
description: Combining evolutionary conservation and proteomics to assess prokaryotic gene predictions | MOTIVATION:A core task of genomics is to identify the boundaries of protein coding genes, which may cover over 90% of a prokaryote's genome. Several programs are available for gene finding, yet it is currently unclear how well these programs perform and whether any offers superior accuracy. This is in part because there is no universal benchmark for gene finding and, therefore, most developers select their own benchmarking strategy. RESULTS:Here, we introduce AssessORF, a new approach for benchmarking prokaryotic gene predictions based on evidence from proteomics data and the evolutionary conservation of start and stop codons. We applied AssessORF to compare gene predictions offered by GenBank, GeneMarkS-2, Glimmer, and Prodigal on genomes spanning the prokaryotic tree of life
feature list: operation 2454
license: GPL-3.0

Assexon
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0194
application sub category: topic_0196
application sub category: topic 3512
citation: https://doi.org/10.1177/1176934319874792
citation: pmcid:PMC6732846
citation: pubmed:31523128
description: Assembling Exon Using Gene Capture Data | Exon capture across species has been one of the most broadly applied approaches to acquire multi-locus data in phylogenomic studies of non-model organisms. Methods for assembling loci from short-read sequences (eg, Illumina platforms) that rely on mapping reads to a reference genome may not be suitable for studies comprising species across a wide phylogenetic spectrum; thus, de novo assembling methods are more generally applied. Current approaches for assembling targeted exons from short reads are not particularly optimized as they cannot (1) assemble loci with low read depth, (2) handle large files efficiently, and (3) reliably address issues with paralogs. Thus, we present Assexon: a streamlined pipeline that de novo assembles targeted exons and their flanking sequences from raw reads
feature list: operation_0524
feature list: operation 3192
feature list: operation 3644

AstroDot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0634
application sub category: topic 3512
citation: jcs.239756
citation: pubmed:32079659
description: A new method for studying the spatial distribution of mRNA in astrocytes | Abstract Cells with a complex shape often use mRNA distribution and local translation to regulate distal functions. These mechanisms have recently been described in astrocytes, the processes of which contact and functionally modulate neighbouring synapses and blood vessels. In order to study the distribution of mRNA in astrocytes, we developed a three-dimensional histological method that combines mRNA detection via in situ hybridization with immunostaining of the astrocyte-specific intermediate filament glial fibrillary acidic protein (GFAP). Three-dimensional confocal images were analyzed using AstroDot, a custom Image J plug-in developed in-house for the identification and quantification of mRNAs in GFAP-immunolabelled astrocyte somata, large processes and fine processes
feature list: operation 2495
feature list: operation 3629

Astrocyte Quantification and Analysis (AQuA)
type: SoftwareApplication
input: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3591
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2333
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Library
application sub category: topic 2229
application sub category: topic 3474
citation: s41593-019-0492-2
citation: pmcid:PMC6858541
citation: pubmed:31570865
description: An event-based tool for analyzing and quantifying calcium or glutamate imaging data.
feature list: operation 3443
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: view

AsyRW
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic 1775
application sub category: topic 3168
citation: TCBB.2019.2943342
citation: pubmed:31562099
description: Cross-Species Protein Function Prediction with Asynchronous-Random Walk | Description :This page includes the codes of AsyRW which are implemented and tested on Matlab2015b version by Ms. Zhao (YingWen Zhao, Email: ywzhao@email.swu.edu.cn) and free for academic usage. You can run it at your own risk. For other purposes, please contact the corresponding author Dr. Yu (Guoxian Yu, Email: gxyu@swu.edu.cn). If you have any problem on using these codes, just contact Dr. Yu or Ms. Zhao via Email
feature list: operation 1777

AtFusionDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: bay135
citation: pmcid:PMC6323297
citation: pubmed:30624648
description: Database of fusion transcripts in Arabidopsis thaliana.
feature list: operation_0224
feature list: operation_0495
feature list: operation 2495
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
primary contact: Dr. Shailesh Kumar

AtacWorks
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic_0769
application sub category: topic 3169
application sub category: topic 3173
application sub category: topic 3474
citation: https://doi.org/10.1101/829481
description: A deep convolutional neural network toolkit for epigenomics. SDK for deep learning based processing of Atac-seq data. AtacWorks is a deep learning toolkit for track denoising and peak calling from low-coverage or low-quality ATAC-Seq data. AtacWorks trains a deep neural network to learn a mapping between noisy (low coverage/low quality) ATAC-Seq data and matching clean (high coverage/high quality) ATAC-Seq data from the same cell type. Once this mapping is learned, the trained model can be applied to improve other noisy ATAC-Seq datasets
feature list: operation_0438
feature list: operation 3222
feature list: operation 3436

Atacama Database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3297
application sub category: topic 3300
application sub category: topic 3697
citation: S10482-019-01328-X
citation: pubmed:31535335
description: a platform of the microbiome of the Atacama Desert | The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information
feature list: operation_0337

AtbPpred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 2269
application sub category: topic 2830
citation: J.CSBJ.2019.06.024
citation: pmcid:PMC6658830
citation: pubmed:31372196
description: A Robust Sequence-Based Prediction of Anti-Tubercular Peptides Using Extremely Randomized Trees | Welcome to the Home Page of AtbPpred | AtbPpred is a web based two-layer prediction server for anti-tubercular peptides. In the first layer, we applied a two-step feature selection procedure and identified the optimal feature set individually for nine different feature encodings, whose corresponding models were developed using extremely randomized tree (ERT). In the second-layer, the predicted probability of AtbPs from the above nine models were considered as input features to ERT and developed the final predictor. For a given peptide, AtbPpred predicts its class and probability values

Atropos
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0196
application sub category: topic 3168
citation: PEERJ.PREPRINTS.2452V2
citation: pmcid:PMC5581536
citation: pubmed:28875074
description: specific, sensitive, and speedy trimming of sequencing reads. An NGS read trimming tool that is specific, sensitive, and speedy. (production). Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. It is a fork of the venerable Cutadapt read trimmer (https://github.com/marcelm/cutadapt, DOI:10.14806/ej.17.1.200), with the primary improvements being:
feature list: operation 3192
feature list: operation 3198
feature list: operation 3219
feature list: operation 3472

Augur
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3474
citation: s41587-020-0605-1
citation: pmcid:PMC7610525
citation: pubmed:32690972
description: Cell type prioritization in single-cell data. Augur is an R package to prioritize cell types involved in the response to an experimental perturbation within high-dimensional single-cell data. The intuition underlying Augur is that cells undergoing a profound response to a given experimental stimulus become more separable, in the space of molecular measurements, than cells that remain unaffected by the stimulus. Augur quantifies this separability by asking how readily the experimental sample labels associated with each cell (e.g., treatment vs. control) can be predicted from molecular measurements alone. This is achieved by training a machine-learning model specific to each cell type, to predict the experimental condition from which each individual cell originated. The accuracy of each cell type-specific classifier is evaluated in cross-validation, providing a quantitative basis for cell type prioritization
feature list: operation 2428
feature list: operation 3450
feature list: operation 3799
license: MIT

Auto-CHO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 2830
application sub category: topic 3314
citation: https://doi.org/10.3791/59987
citation: pubmed:31545316
description: Hierarchical and Programmable One-Pot Oligosaccharide Synthesis | Auto-CHO is a free-to-use software for providing glycan synthetic solutions by one-pot approach | Auto-CHO is an open source (MIT License) and free-to-use software developed by Academia Sinica for providing solutions of hierarchical one-pot glycan synthesis | Auto-CHO is an open source (MIT Licence) and free-to-use software developed by Academia Sinica for providing solutions of hierarchical one-pot glycan synthesis
license: MIT

AutoEncoder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3295
application sub category: topic 3474
citation: S12864-019-6285-X
citation: pmcid:PMC6923820
citation: pubmed:31856727
description: Integrate multi-omics data with biological interaction networks using Multi-view Factorization AutoEncoder (MAE).
feature list: operation 2492
feature list: operation 3439
feature list: operation 3659
license: MIT

AutoGridFR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0219
application sub category: topic 2275
citation: JCC.26054
citation: pubmed:31436329
description: Improvements on AutoDock Affinity Maps and Associated Software Tools | Precomputed affinity maps are used by AutoDock to efficiently describe rigid biomolecules called receptors in automated docking. These maps greatly speed up the docking process and allow users to experiment with the forcefield. Here, we present AutoGridFR (AGFR): a software tool facilitating the calculation of these maps. We describe a new version of the AutoSite algorithm that improves the description of binding pockets automatically detected on receptors, and an algorithm for adding affinity gradients which help search methods optimize solution using fewer evaluations of the scoring functions. AGFR supports the calculation of maps for various advanced docking techniques such as covalent docking, hydrated docking, and docking with flexible receptor sidechains
feature list: operation_0482
feature list: operation 3216
feature list: operation 3899

AutoPVS1
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3168
application sub category: topic 3320
citation: humu.24051
citation: pubmed:32442321
description: An automatic classification tool for PVS1 interpretation of null variants | Abstract Null variants are prevalent within human genome, and their accurate interpretation is critical for clinical management. In 2018, the ClinGen Sequence Variant Interpretation (SVI) Working Group refined the only criterion (PVS1) for pathogenicity in the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG AMP) guidelines. The refinement may improve interpretation consistency, but it also brings hurdles to biocurators because of the complicated workflows and multiple bioinformatics sources required. To address these issues, we developed an automatic classification tool called AutoPVS1 to streamline PVS1 interpretation. We assessed the performance of AutoPVS1 using 56 variants manually curated by ClinGen’s SVI Working Group and achieved an interpretation concordance of 95% (53 56)
feature list: operation 3225

AutoTuner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3172
application sub category: topic 3407
application sub category: topic 3520
citation: acs.analchem.9b04804
citation: pmcid:PMC7310949
citation: pubmed:32212641
description: Autotuner is a used to identify proper parameters during metabolomics data processing.
feature list: operation 3215
license: MIT

Autopilot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3361
application sub category: topic 3678
citation: https://doi.org/10.1101/807693
description: A complete, open-source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Autopilot enables qualitatively greater experimental flexibility by allowing arbitrary numbers of hardware components to be combined in arbitrary experimental designs.
license: MPL-2.0

Axiom Analysis Suite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Suite
application sub category: topic 2885
application sub category: topic 3518
application sub category: topic 3810
citation: S12864-019-5712-3
citation: pmcid:PMC6498479
citation: pubmed:31046664
description: Axiom Analysis Suite advances genotyping data analysis with a single-source software package to enable complete genotyping analysis of all Axiom arrays and copy number analysis on select Axiom arrays.
feature list: operation_0308
feature list: operation_0484
feature list: operation 3196
is accessible for free: true
license: Unlicense
operating system: Windows
software help: Axiom Analysis Suite v 4.0.1 User Guide.pdf
primary contact: 0000-0001-9224-056X

B-SOiD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3474
citation: https://doi.org/10.1101/770271
description: An Open Source Unsupervised Algorithm for Discovery of Spontaneous Behaviors | Behavioral segmentation of open field in DeepLabCut, or B-SOID ("B-side"), is an unsupervised learning algorithm written in MATLAB that serves to discover behaviors that are not pre-defined by users | B-SOID: Behavioral segmentation of open field in DeepLabCut
feature list: operation 3891
license: GPL-3.0

BACMMAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic 3382
application sub category: topic 3855
citation: S41596-019-0216-9
citation: pubmed:31554957
description: High-throughput detection and tracking of cells and intracellular spots in mother machine experiments | BACteria in Mother Maching Analyzer (BACMMAN) is a software allowing fast and reliable automated image analysis of high-throughput 2D/3D time-series images from mother machine. Mother machine is a very popular microfluidic device allowing investigating biological processes in bacteria at the single-cell level | BACMMAN: BACteria in Mother Machine Analyzer | BACMMAN was designed to analyse data from Mother machine experiments
feature list: operation 3443
license: GPL-3.0
software help: wiki

BAGSE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 2269
application sub category: topic 3170
application sub category: topic 3517
citation: btz831
citation: pmcid:PMC7523653
citation: pubmed:31702789
description: A Bayesian Hierarchical Model Approach for Gene Set Enrichment Analysis. Bayesian Analysis of Gene Set Enrichment. This repository contains the software package BAGSE designed for gene set enrichment analysis. BAGSE performs both enrichment (hypothesis) testing and quantification. It requires gene-level association evidence (in forms of either z-scores or estimated effect sizes with corresponding standard errors) and pre-defined gene set annotations as input
feature list: operation 2436
feature list: operation 3658
feature list: operation 3659
feature list: operation 3799

BAM-matcher
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3168
application sub category: topic 3518
citation: btw239
citation: pubmed:27153667
description: Tool that determines if two BAM files came from the same sample or patient by comparing common SNP positions.
feature list: operation 3196
feature list: operation 3501
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
software help: Home
primary contact: Paul P.S. Wang

BAMM-SC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 2229
application sub category: topic 3308
application sub category: topic 3474
citation: s41467-019-09639-3
citation: pmcid:PMC6456731
citation: pubmed:30967541
description: Bayesian mixture model for single-cell sequencing (BAMM-SC) method for clustering droplet-based single cell transcriptomic data from population studies.
feature list: operation 3216
feature list: operation 3431
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software version: 1.0.0
primary contact: Li Chen
primary contact: Zhe Sun

BAMixChecker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3673
application sub category: topic 3676
citation: btz479
citation: pmcid:PMC6853765
citation: pubmed:31197312
description: Automated checkup tool for matched sample pairs in NGS cohort.
feature list: operation_0484
feature list: operation 3196
is accessible for free: true
operating system: Linux
software help: latest

BANDITS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3320
citation: s13059-020-01967-8
citation: pmcid:PMC7075019
citation: pubmed:32178699
description: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty | BANDITS: Bayesian ANalysis of DIfferenTial Splicing | BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts
feature list: operation_0264
feature list: operation 3223
feature list: operation 3800
license: GPL-3.0

BART-Seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0632
application sub category: topic 3170
application sub category: topic 3308
citation: S13059-019-1748-6
citation: pmcid:PMC6683345
citation: pubmed:31387612
description: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis | Software required for Bart-Seq technology – a cheap technology to analyze (single) cells using forward and reverse barcoding for target genes | Demultiplexing pipeline for BARTSeq | Software required for Bart-Seq – a cost-effective target enrichment technology using forward and reverse barcoding to analyze selected set of genes in single cells and/or bulk RNA/DNA samples | The pipeline can be run via snakemake [-j 4] [-s …/bartseq/Snakefile] [-d …/mydata], where -j specifies the number of threads, and the other parameters default to ./Snakefile and ., respectively
feature list: operation_0308
feature list: operation 3192
feature list: operation 3200
license: GPL-3.0

BASILIScan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic_0593
application sub category: topic 3538
citation: s12864-018-5322-5
citation: pmcid:PMC6290515
citation: pubmed:30537929
description: Tool for high-throughput analysis of intrinsic disorder patterns in homologous proteins.
feature list: operation_0250
feature list: operation_0337
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: faqs
software help: readme
software help: tutorial
primary contact: M. Barski

BBCancer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3512
citation: gkz942
citation: pmcid:PMC7145713
citation: pubmed:31665503
description: an expression atlas of blood-based biomarkers in the early diagnosis of cancers. The early detection of cancer holds the key to combat and control the increasing global burden of cancer morbidity and mortality. Blood-based screenings using circulating DNAs (ctDNAs), circulating RNA (ctRNAs), circulating tumor cells (CTCs) and extracellular vesicles (EVs) have shown promising prospects in the early detection of cancer. Recent high-throughput gene expression profiling of blood samples from cancer patients has provided a valuable resource for developing new biomarkers for the early detection of cancer. However, a well-organized online repository for these blood-based high-throughput gene expression data is still not available
feature list: operation_0463
feature list: operation 2495
feature list: operation 3435

BCIgEPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
author: https://orcid.org/0000-0001-5145-0384
citation: S0026898418020180
citation: pubmed:29695703
description: BCIgePred (Linear B cell IgE Epitope Predictor) is a perl based open source tool for the prediction of Linear B-cell IgE epitopes.
feature list: operation 2423
is accessible for free: true
license: GPL-3.0
operating system: Linux

BCSExplorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0821
application sub category: topic 3047
application sub category: topic 3172
application sub category: topic 3343
citation: BTZ755
citation: pubmed:31593245
description: A Customized Biosynthetic Chemical Space Explorer with Multifunctional Objective Function Analysis. Select all Deselect all Toggle select. ( Note:The less enzymes/biotransformations you select, the shorter the runtime is.)
feature list: operation 3564

BCrystal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0121
application sub category: topic 2828
citation: btz762
citation: pmcid:PMC7523644
citation: pubmed:31603511
description: An Interpretable Sequence-Based Protein Crystallization Predictor. The training set is readily available for ease of use at: https://drive.google.com/file/d/1FRWIcs4xvK2O5OCqhg7u5g_4qm2zJn2d/view and can be used in combination with Step 2 to generate the BCrystal model
feature list: operation_0267
feature list: operation_0303
feature list: operation_0410
feature list: operation_0420
feature list: operation 3454

BDE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3047
application sub category: topic 3314
application sub category: topic 3407
application sub category: topic 3474
citation: chemrxiv.10052048.v2
description: Prediction of Homolytic Bond Dissociation Enthalpies for Organic Molecules at near Chemical Accuracy with Sub-Second Computational Cost.
feature list: operation_0394
feature list: operation_0417
feature list: operation 3439

BEACON
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0091
application sub category: topic_0204
application sub category: topic 3474
citation: https://doi.org/10.1101/2024.10.17.618926
citation: pmcid:PMC11527036
citation: pubmed:39484404
description: BEACON is a computational framework designed to perform Bayesian analysis on expression and gene dependency data across different cell lineages. The model integrates expression as the dependent variable and gene dependency data as the independent variable. The framework uses JAGS (Just Another Gibbs Sampler) for Bayesian inference and MCMC (Markov Chain Monte Carlo) simulations to estimate parameters of interest, including the correlation between gene expression and dependency.
feature list: operation 3463
license: MIT
software help: readme
primary contact: Kuan-lin Huang

BEAN-counter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic 3168
application sub category: topic 3343
citation: s41596-018-0099-1
citation: pmcid:PMC6818255
citation: pubmed:30635653
description: Pipeline for processing barcode sequencing data from multiplexed experiments. Applicable to any experiment in which pools of genetically barcoded cells are grown under different conditions, with the resulting barcode DNA isolated from those cells combined into one 2nd-gen sequencing run via the use of indexed PCR primers.
feature list: operation 3192
feature list: operation 3200
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: barseqcounterdocs
primary contact: Myers Lab

BEERE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic 3063
citation: GKZ428
citation: pmcid:PMC6602520
citation: pubmed:31114876
description: Tool for Biomedical Entity Expansion, Ranking, and Exploration.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3280
is accessible for free: true
license: CC-BY-NC-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: Jake Y Chen

BEL Commons
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic 3855
citation: bay126
citation: pmcid:PMC6301338
citation: pubmed:30576488
description: Environment for exploration and analysis of networks encoded in Biological Expression Language.
feature list: operation 1812
feature list: operation 3083
feature list: operation 3501
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: about

BERMUDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 3170
citation: S13059-019-1764-6
citation: pmcid:PMC6691531
citation: pubmed:31405383
description: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes | BERMUDA (Batch Effect ReMoval Using Deep Autoencoders) is a novel transfer-learning-based method for batch correction in scRNA-seq data | BERMUDA: Batch Effect ReMoval Using Deep Autoencoders
feature list: operation 3680
feature list: operation 3800
license: MIT

BEable-GPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3168
application sub category: topic 3512
application sub category: topic 3912
citation: S13059-019-1839-4
citation: pmcid:PMC6806563
citation: pubmed:31647030
description: BEable-GPS: Base Editable prediction of Global Pathogenic-related SNVs. Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs.
feature list: operation 2421
feature list: operation 3096
feature list: operation 3461
license: MIT

BGSC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic 3320
application sub category: topic 3523
citation: S12859-019-2944-9
citation: pmcid:PMC6704634
citation: pubmed:31438847
description: Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line | Bayesian Gene Selection Criterion (BGSC) approach | The datasets analyzed during the current study are available in the BGSC repository. The raw data files are in the folder rawdata including the Einzelanalyse_nonorm_nobkgd_SF767-1.txt.gz and ControlProbeProfile_SF767-1.txt.gz. The lists of genes predicted for all of the four classes can be found in the folder PredectionResult
feature list: operation 3223

BGSVM-NUC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic 3125
application sub category: topic 3534
citation: https://doi.org/10.2174/1386207322666190925125524
citation: pubmed:31553288
description: Boosting Granular Support Vector Machines for the Accurate Prediction of Protein-Nucleotide Binding Sites | AIM AND OBJECTIVE:The accurate identification of protein-ligand binding sites helps elucidate protein function and facilitate the design of new drugs. Machine-learning-based methods have been widely used for the prediction of protein-ligand binding sites. Nevertheless, the severe class imbalance phenomenon, where the number of nonbinding (majority) residues is far greater than that of binding (minority) residues, has a negative impact on the performance of such machine-learning-based predictors. MATERIALS AND METHODS:In this study, we aim to relieve the negative impact of class imbalance by boosting multiple granular support vector machines (BGSVM). In BGSVM, each base SVM is trained on a granular training subset consisting of all minority samples and some reasonably selected majority samples
feature list: operation_0482
feature list: operation 2575

Bovine Genome Variation Database (BGVD)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0621
application sub category: topic 2885
application sub category: topic 3056
application sub category: topic 3168
citation: https://doi.org/10.1101/802223
description: An integrated Web-database for bovine sequencing variations and selective signatures.
feature list: operation_0487
feature list: operation 2421
feature list: operation 2422
feature list: operation 3196
feature list: operation 3208

BIGSI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0196
application sub category: topic_0622
application sub category: topic 3673
citation: s41587-018-0010-1
citation: pubmed:30718882
description: BItsliced Genomic Signature Index (BIGSI) searches a collection of raw (fastq/bam), contigs or assembly for genes, variant alleles and arbitrary sequence.
feature list: operation 3211
feature list: operation 3431
feature list: operation 3840
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: bigsi.readme.io
primary contact: Phelim Bradley

BINDER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic_0749
citation: S12859-019-3042-8
citation: pmcid:PMC6734328
citation: pubmed:31500560
description: Computationally inferring a gene regulatory network for Mycobacterium abscessus | BINDER (BayesIan gene regulatory Networks inferreD via gene coExpression and compaRative genomics) is a hybrid approach, integrating coexpression and comparative genomics to infer prokaryotic regulons | Code, data and results for 'BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus'
feature list: operation_0277
feature list: operation 1781
feature list: operation 3439
license: GPL-3.0

BIRD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic 2269
citation: btz545
citation: pmcid:PMC7999138
citation: pubmed:31368479
description: Bayesian Estimation of Genetic Regulatory Effects in High-throughput Reporter Assays | Bayesian Inference of Regulatory Differences | Photo by Bill Majoros. Used with permission | [6/16/2018] First version of BIRD released - The first version of BIRD has been released on GitHub at https://github.com/bmajoros/BIRD | [8/23/2018] Experiment design web tool released - A web tool is now available for power and sample size estimation: http://67.159.92.22:8080/ | BIRD (Bayesian Inference of Regulatory Differences) is a software suite for identifying regulatory variants in data from STARR-seq and other massively parallel reporter assays (MPRAs)
feature list: operation_0488
feature list: operation 3196
feature list: operation 3227

BIII (BioImage Informatics Index, biii.eu)
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2330
input: Ontology term
  type: FormalParameter
  additional type: data_0966
  encoding format: format 2330
output: Resource metadata
  type: FormalParameter
  additional type: data 2337
  encoding format: format 2331
  encoding format: format 3464
output: Training material
  type: FormalParameter
  additional type: data 3669
  encoding format: format 2331
  encoding format: format 3464
output: Workflow metadata
  type: FormalParameter
  additional type: data_0949
  encoding format: format 2331
  encoding format: format 3464
output: Ontology concept definition
  type: FormalParameter
  additional type: data 1731
  encoding format: format 2331
  encoding format: format 3464
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
additional type: Database portal
additional type: Web application
application sub category: topic_0091
application sub category: topic_0769
application sub category: topic 3063
application sub category: topic 3298
application sub category: topic 3382
contributor: 0000-0001-6926-191X
contributor: https://orcid.org/0000-0002-1509-4981
contributor: https://orcid.org/0000-0002-2411-0429
contributor: https://orcid.org/0000-0002-3597-8557
contributor: https://orcid.org/0000-0002-4009-6225
contributor: Chong Zhang
description: BIII (BioImage Informatics Index, biii.eu) is a registry of software tools, image databases for benchmarking, and training materials for bioimage analysis. Software tools are organized as either a full protocol of analysis (workflow), a specific component to construct a workflow, or a software platform or library (collection). They are described using EDAM-bioimaging. All entries are exposed following FAIR principles and accessible for other usage with ODC-By v1.0 license.
feature list: operation_0224
feature list: operation 3761
is accessible for free: true
license: Other
provider: NEUBIAS Network of Bioimage Analysts
software help: http://biii.eu/soft
software help: http://visualdataweb.de/webvowl/
software help: howtocurate
software help: EDAM-BIOIMAGING
software help: wiki
primary contact: 0000-0002-4822-165X

BISON
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3384
application sub category: topic 3444
citation: mrm.28547
citation: https://doi.org/10.1101/747998
citation: pubmed:33040404
description: Brain tISue segmentatiON pipeline using T1-weighted magnetic resonance images and a random forests classifier | Abstract Introduction Accurate differentiation of brain tissue types from T1-weighted magnetic resonance images (MRIs) is a critical requirement in many neuroscience and clinical applications. Accurate automated tissue segmentation is challenging due to the variabilities in the tissue intensity profiles caused by differences in scanner models and acquisition protocols, in addition to the varying age of the subjects and potential presence of pathology. In this paper, we present BISON (Brain tISue segmentatiON), a new pipeline for tissue segmentation. Methods BISON performs tissue segmentation using a random forests classifier and a set of intensity and location priors obtained based on T1-weighted images

BISR-RNAseq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3316
citation: S12859-019-3251-1
citation: pmcid:PMC6923898
citation: pubmed:31861980
description: An efficient and scalable RNAseq analysis workflow with interactive report generation. BISR-RNAseq pipeline submitted for ICIBM-2019. Submission files for the ICIBM2019 conference
feature list: operation_0337
feature list: operation 3211
feature list: operation 3680
license: LGPL-3.0

BITACORA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0623
application sub category: topic 3512
citation: https://doi.org/10.1101/593889
citation: https://doi.org/10.1111/1755-0998.13202
citation: pubmed:32492257
description: A comprehensive tool for the identification and annotation of gene families in genome assemblies | BITACORA: A Bioinformatics tool for gene family annotation | Genome annotation is a critical bottleneck in genomic research, especially for the rigorous and comprehensive study of gene families in the genomes of non-model organisms | BITACORA: A pipeline for the identification and annotation of gene families in genome assemblies | Genome annotation is a critical bottleneck in genomic research, especially for the rigorous and comprehensive study of gene families
feature list: operation_0525
feature list: operation 3192
feature list: operation 3216
license: GPL-3.0

BJASS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: https://doi.org/10.1177/0962280219864710
citation: pmcid:PMC8285086
citation: pubmed:31359834
description: A new joint screening method for right-censored time-to-event data with ultra-high dimensional covariates | Liu, Y., Chen, X., & Li, G. (2019). A new joint screening method for right-censored time-to-event data with ultra-high dimensional covariates. Statistical methods in medical research, 0962280219864710 | This program implements the BJASS joint screening method for DLBCL data (stored in matlab.mat) described in Section 4 of the paper
feature list: operation 3501
feature list: operation 3557
feature list: operation 3659

BLANT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0602
citation: btz603
citation: pubmed:31373347
description: Basic Local Alignment for Networks Tool.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Wayne B. Hayes

BLINK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic 3517
application sub category: topic 3810
citation: giy154
citation: pmcid:PMC6365300
citation: pubmed:30535326
description: Package for the next level of genome-wide association studies.
feature list: operation_0282
feature list: operation 3196
feature list: operation 3798
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Meng Huang
primary contact: Yao Zhou

BLMRM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 2269
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3512
citation: S12859-019-3141-6
citation: pmcid:PMC6819473
citation: pubmed:31660858
description: Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model. A R package to perform genome-wide allele-specific expression. BLMRM: A Bayesian Logistic Regression Model for Genome-Wide Detection of Allele-Specific Gene Expression. This R package provide a powerful and flexiable method (BLMRM) to detect ASE genes and detect ASE variation within genes simultaneously while maintaining low computational requirements
feature list: operation_0484
feature list: operation 3196
feature list: operation 3659

BLUES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0176
application sub category: topic 3306
application sub category: topic 3314
application sub category: topic 3315
citation: acs.jpcb.7b11820
citation: CHEMRXIV.5406907.V2
citation: CHEMRXIV.5406907.V3
citation: CHEMRXIV.5406907.V4
citation: CHEMRXIV.5406907.V5
citation: pmcid:PMC5980761
citation: pubmed:29486559
description: Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo. Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling. BLUES: Binding modes of Ligands Using Enhanced Sampling. Gill, S; Lim, N. M.; Grinaway, P.; Rustenburg, A. S.; Fass, J.; Ross, G.; Chodera, J. D.; Mobley, D. L. “Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo” - Journal of Physical Chemistry B. February 27, 2018
feature list: operation_0482
feature list: operation 2476
feature list: operation 3899
license: MIT

BMCeasy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0202
application sub category: topic 2840
application sub category: topic 3315
application sub category: topic 3360
citation: ALTEX.1912021
citation: pubmed:31833558
description: Determination of benchmark concentrations and their statistical uncertainty for cytotoxicity test data and functional in vitro assays.
feature list: operation 3435
feature list: operation 3503
feature list: operation 3799
software help: bmc.pdf

BMEG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3173
citation: https://doi.org/10.1101/773911
citation: CCI.19.00110
citation: pmcid:PMC7049249
citation: pubmed:32097025
description: Exploring Integrative Analysis using the BioMedical Evidence Graph | A graph database for merging and analyzing connected data | Discover The BMEG is a graph database that collects data from over 20 different large scale resources and aggregates them into a single coherent resource. Sources include:
feature list: operation_0224
feature list: operation 3436
feature list: operation 3501

BMRF-Net
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0128
application sub category: topic 2640
application sub category: topic 3518
citation: btv137
citation: pmcid:PMC4495295
citation: pubmed:25755273
description: Software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
primary contact: Jianhua Xuan

BMSS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3315
citation: ACSSYNBIO.8B00523
citation: pubmed:31035759
description: Automated BioModel Selection System for gene circuit designs, supports bio-model automated fitting and selection processes, providing a means to efficiently derive the best model candidate that could capture the transient (time-series) dynamic profiles of a bio-part or device using characterization data.
feature list: operation 2426
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: BMSS User Manual.pdf

BMTME
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 3810
application sub category: topic 3855
citation: g3.119.400126
citation: pubmed:30819822
description: R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Based Prediction.
feature list: operation 3557
feature list: operation 3659
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: BMTME
primary contact: Francisco Javier Luna-Vazquez

BNNR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0209
application sub category: topic 3377
application sub category: topic 3379
citation: BTZ331
citation: pmcid:PMC6612853
citation: pubmed:31510658
description: Drug repositioning based on bounded nuclear norm regularization | BNNR is a novel computational method, which utilizes Bounded Nuclear Norm Regularization algorithm to identify potential novel indications for known or new drugs. The code in this package implements Bounded Nuclear Norm Regularization (BNNR) for drug repositioning, which is implemented in Matlab2014a

BO-LSTM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic_0602
citation: s12859-018-2584-5
citation: pmcid:PMC6323831
citation: pubmed:30616557
description: Model to detect and classify relations in text, representing each entity of domain-specific ontologies as the sequence of its ancestors in the ontology. BO-LSTM is implemented as a recurrent neural network with long short-term memory units and using open biomedical ontologies.
feature list: operation 3280
feature list: operation 3625
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
primary contact: BioTM

BOCS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3360
citation: https://doi.org/10.1101/631333
description: Simulation that applies bioinformatics algorithm – block optical content scoring (BOCS) – which uses DNA k-mer content for rapid, broad-spectrum identification of genetic biomarkers.
feature list: operation 3482
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Lee Korshoj

BONITA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3308
application sub category: topic 3336
citation: JOURNAL.PCBI.1007317
citation: pmcid:PMC6743792
citation: pubmed:31479446
description: Executable pathway analysis using ensemble discrete-state modeling for large-scale data | BONITA- Boolean Omics Network Invariant-Time Analysis is a package for the inference of Boolean rules and pathway analysis on omics data. It can be applied to help uncover underlying relationships in biological data. Please see our publication for more information: [insert eventual publication here]
feature list: operation 2497
feature list: operation 3501
feature list: operation 3562

BOOSTER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0084
description: BOOSTER is an alternative method for calculating the branch supports of phylogenetic trees, using the bootstrap. With large trees and moderate phylogenetic signal, BOOSTER tends to be more informative than the standard Felsenstein bootstrap method.

BORIS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0602
application sub category: topic 3305
application sub category: topic 3324
citation: https://doi.org/10.1101/835421
citation: journal.pone.0235660
citation: pmcid:PMC7363093
citation: pubmed:32667952
description: BORIS: R package for Bayesian Outbreak Reconstruction Inference and Simulation. Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates.
feature list: operation_0451
feature list: operation 3660
license: GPL-2.0

Brain Predictability toolbox
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0769
application sub category: topic 3300
application sub category: topic 3384
application sub category: topic 3474
citation: btaa974
citation: pmcid:PMC8485846
citation: pubmed:33216147
description: The Brain Predictability toolbox (BPt) is a Python based Machine Learning library designed for working with Neuroimaging data. This library is particularly suited towards working with large neuroimaging datasets, where a large number of subjects with potentially multimodal data are avaliable.
feature list: operation_0224
feature list: operation 3359
feature list: operation 3659
license: MIT
software help: latest

BRAPeS
type: SoftwareApplication
input: Sequence alignment (nucleic acid)
  type: FormalParameter
  additional type: data 1383
  encoding format: format 2572
output: Sequence report
  type: FormalParameter
  additional type: data 2955
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 2830
citation: https://doi.org/10.1101/389999
description: Software for reconstruction of B cell receptors (BCR) using short, paired-end single-cell RNA-sequencing.
feature list: operation_0230
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Shaked Afik

BRIE
type: SoftwareApplication
input: Sequence alignment (nucleic acid)
  type: FormalParameter
  additional type: data 1383
  encoding format: format 2572
output: Nucleic acid report
  type: FormalParameter
  additional type: data 2084
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3320
citation: 978-1-4939-9057-3 12
citation: s13059-017-1248-5
citation: pmcid:PMC5488362
citation: pubmed:28655331
citation: pubmed:30758827
description: Bayesian method for estimating splicing isoform proportions from single cell RNA-seq data.
feature list: operation 2499
feature list: operation 3800
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: install.html
software help: manual.html
primary contact: Yuanhua Huang

BRM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0659
application sub category: topic 3518
citation: S12859-019-2805-6
citation: pmcid:PMC6525352
citation: pubmed:31101000
description: Systems biology web tool for microRNA and omics data integration.
feature list: operation_0463
feature list: operation 1812
feature list: operation 2422
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial.html
primary contact: https://orcid.org/0000-0002-5427-6462
primary contact: Katrina M. Waters

Block Regression Mapping (BRM)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 2269
application sub category: topic 2885
citation: BTZ861
citation: pubmed:31742317
description: Block Regression Mapping (BRM) is a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing.
feature list: operation_0282
feature list: operation_0283
feature list: operation 3196
feature list: operation 3435
feature list: operation 3659
license: GPL-3.0

BRUSELAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0154
application sub category: topic 3316
application sub category: topic 3336
citation: ACS.JCIM.9B00279
citation: pubmed:31074975
description: HPC Generic and Customizable Software Architecture for 3D Ligand-Based Virtual Screening of Large Molecular Databases.
feature list: operation_0482
feature list: operation 3216
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: FAQ.php
software help: Tutorial.php
primary contact: Horacio Pérez-Sánchez

BSA4Yeast
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 3168
citation: GIZ060
citation: pmcid:PMC6571488
citation: pubmed:31141611
description: Web-based quantitative trait locus linkage analysis and bulk segregant analysis of yeast sequencing data.
feature list: operation_0282
feature list: operation 1812
feature list: operation 3232
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Use
primary contact: Zhi Zhang

BSGatlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3170
application sub category: topic 3512
citation: https://doi.org/10.1101/807263
description: An enhanced annotation of genes and transcripts for the Bacillus subtilis genome with improved information access. On this website we provide access to our annotation integration efforts for Bacillus subtilis 168. We integrated the gene annotations from BsubCyc, Rfam, RefSeq, SubtiWiki, and some additional resources (see manuscript for details). Each gene indicates from which reources its annotation stem from, and links to the respective resources are provided where applicable. The integration overall improved the annotation of non-coding RNAs (ncRNA) in B. subtilis. Based on public transcription start sites (TSS) and termination sites (TTS), we created a comprehensive annotation of operons, transcripts, and transcriptional units (TU) for 93% of the genes in the genome. We provide the BSGatlas in form of a UCSC browser hub, a downloadable GFF3 file, and as a light-weight interactive quick browser directly on this side
feature list: operation_0362
feature list: operation_0435
feature list: operation 2422

BUGSnet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0621
application sub category: topic 3068
citation: S12874-019-0829-2
citation: pmcid:PMC6805536
citation: pubmed:31640567
description: an R package to facilitate the conduct and reporting of Bayesian network Meta-analyses. Bayesian inference Using Gibbs Sampling to conduct NETwork meta-analysis”]. BUGSnet: Bayesian inference Using Gibbs Sampling to conduct NETwork meta-analysis. [Home] [Installation] [RStudio Server] [Vignettes]. BUGSnet is a new feature-rich R package to conduct high-quality Bayesian NMA analyses and facilitate compliance with best practice guidelines and reporting. Bayesian analyses are conducted with JAGS (BUGS code is automatically generated by the package based on the user’s inputs.) Outputs are highly customizable and include network plots, tables of network characteristics, data plots, league tables and league heat plots, SUCRA plots, rankograms, forest plots, leverage plots, traceplots and posterior mean deviance comparison plots
feature list: operation 2238
feature list: operation 3436

BUStools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: BTZ279
citation: pubmed:31073610
description: > COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/pymzml (GITHUB.COM) | > CORRECT NAME OF TOOL COULD ALSO BE 'BUStools suite', 'BUStools suite tools', 'BUS' (bio.tools/bus), 'kallisto' (bio.tools/kallisto) | The Barcode, UMI, Set format and BUStools | Materials associated with the manuscript "The Barcode, UMI, Set format and BUStools" by Páll Melsted, Vasilis Ntranos and Lior Pachter | Tools for working with BUS files | R vignettes for processing BUS format single-cell RNA-seq files
feature list: operation 3200
feature list: operation 3680
feature list: operation 3800
is accessible for free: true
license: BSD-2-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: manual
software help: documentation
primary contact: Lior Pachter
primary contact: Páll Melsted
primary contact: Vasilis Ntranos

BVSim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: A Benchmarking Variation Simulator Mimicking Human Variation Spectrum

BWGS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
citation: https://doi.org/10.1101/763037
citation: journal.pone.0222733
citation: pmcid:PMC7141418
citation: pubmed:32240182
description: A R package for genomic selection and its application to a wheat breeding programme | Abstract We developed an integrated R library called BWGS to enable easy computation of Genomic Estimates of Breeding values (GEBV) for genomic selection. BWGS relies on existing R-libraries, all freely available from CRAN servers. The two main functions enable to run 1) replicated random cross validations within a training set of genotyped and phenotyped lines and 2) GEBV prediction, for a set of genotyped-only lines. Options are available for 1) missing data imputation, 2) markers and training set selection and 3) genomic prediction with 15 different methods, either parametric or semi-parametric. The usefulness and efficiency of BWGS are illustrated using a population of wheat lines from a real breeding programme. Adjusted yield data from historical trials (highly unbalanced design) were used for testing the options of BWGS
feature list: operation 3196
feature list: operation 3557

BWMR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0625
application sub category: topic 2269
application sub category: topic 3172
application sub category: topic 3517
citation: BTZ749
citation: pubmed:31593215
description: Bayesian weighted Mendelian randomization for causal inference based on summary statistics. BWMR (Bayesian Weighted Mendelian Randomization). Code for the experiments in BWMR. BWMR (Bayesian Weighted Mendelian Randomization), is an efficient statistical method to infer the causality between a risk exposure factor and a trait or disease outcome, based on GWAS summary statistics. 'BWMR' package provides the estimate of causal effect with its standard error and the P-value under the test of causality
feature list: operation 3435
feature list: operation 3658
feature list: operation 3659

BWView
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3334
description: Application designed to view the frequency content of recorded brainwave files. It uses wavelets rather than a conventional FFT to analyse the data for maximum flexibility and resolution.
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Windows
primary contact: Jim Peters

BacFITBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0736
application sub category: topic_0798
application sub category: topic 3324
citation: gkz931
citation: pmcid:PMC7145566
citation: pubmed:31665505
description: A database to assess the relevance of bacterial genes during host infection. Bacterial Fitness In infecTion dataBase. Host species Any host species Cow (Bos taurus) Chicken (Gallus gallus) Mouse (Mus musculus) Rabbit (Oryctolagus cuniculus) Pig (Sus scrofa) Pathogen Any pathogen Acinetobacter baumannii ATCC 17978 Campylobacter jejuni subsp. jejuni 81-176 Escherichia coli CFT073 Escherichia coli M12 Escherichia coli O157:H7 str. EDL933 Haemophilus influenzae Rd KW20 Klebsiella pneumoniae subsp. pneumoniae ATCC 43816 KPPR1 Mycobacterium avium subsp. paratuberculosis K10 Porphyromonas gingivalis ATCC 33277 Salmonella enterica Serovar Typhimurium SL1344 Salmonella enterica Serovar Typhimurium ST4 74 Serratia marcescens Strain UMH9 Streptococcus pyogenes M1 5448 Vibrio cholerae O1 biovar El Tor str. N16961 Vibrio parahaemolyticus RIMD 2210633
feature list: operation_0418
feature list: operation_0435
feature list: operation 2421

BacHBerryEXP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0196
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3308
citation: S12864-019-6183-2
citation: pmcid:PMC6924045
citation: pubmed:31856735
description: A gene Expression Browser for RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics.
feature list: operation_0524
feature list: operation 3196
feature list: operation 3258

BacTag
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 3305
application sub category: topic 3673
citation: S12864-019-5723-0
citation: pmcid:PMC6501397
citation: pubmed:31060512
description: Pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing.
feature list: operation 1812
feature list: operation 3227
feature list: operation 3840
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: home
primary contact: https://orcid.org/0000-0002-0218-9092

BactMAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2229
application sub category: topic 3382
citation: mmi.14417
citation: pmcid:PMC7027861
citation: pubmed:31693257
description: an R package for integrating, analyzing and visualizing bacterial microscopy data | Abstract High-throughput analyses of single-cell microscopy data is a critical tool within the field of bacterial cell biology. Several programs have been developed to specifically segment bacterial cells from phase-contrast images. Together with spot and object detection algorithms, these programs offer powerful approaches to quantify observations from microscopy data, ranging from cell-to-cell genealogy to localization and movement of proteins. Most segmentation programs contain specific post-processing and plotting options, but these options vary between programs and possibilities to optimize or alter the outputs are often limited. Therefore, we developed BactMAP ( Bac terial t oolbox for M icroscopy A nalysis & P lotting), a software package that allows researchers to transform cell segmentation and spot detection data generated by different programs automatically into various plots

BactSNP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 2885
application sub category: topic 3673
citation: MGEN.0.000261
citation: pmcid:PMC6562250
citation: pubmed:31099741
description: Tool to identify SNPs among bacterial isolates. BactSNP can detect SNPs and create a simple TSV file with SNP information as well as an alignment FASTA file containing reconstructed pseudo-genomes of the target isolates in a one-step process.
feature list: operation_0484
feature list: operation 3216
feature list: operation 3840
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: README.md
primary contact: Takehiko Itoh

Bagging-SVM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3373
application sub category: topic 3474
citation: J.ARTMED.2019.07.005
citation: pubmed:31521251
description: > CORRECT NAME OF TOOL COULD ALSO BE 'genetic algorithm Bagging-SVM', 'druggable', '93.78' | Accurate prediction of potential druggable proteins based on genetic algorithm and Bagging-SVM ensemble classifier | Discovering and accurately locating drug targets is of great significance for the research and development of new drugs. As a different approach to traditional drug development, the machine learning algorithm is used to predict the drug target by mining the data. Because of its advantages of short time and low cost, it has received more and more attention in recent years. In this paper, we propose a novel method for predicting druggable proteins. Firstly, the features of the protein sequence are extracted by combining Chou's pseudo amino acid composition (PseAAC), dipeptide composition (DPC) and reduced sequence (RS), getting the 591 dimension of drug target dataset

BalLeRMix
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0781
application sub category: topic 3420
citation: https://doi.org/10.1101/645887
description: Robust and window-insensitive mixture model approaches for localizing balancing selection.
feature list: operation_0487
feature list: operation 3196
is accessible for free: true
license: Unlicense
operating system: Linux
software help: BalLeRMix manual.pdf
primary contact: Michael DeGiorgio

Banana Genome Hub
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2330
input: Sequence
  type: FormalParameter
  additional type: data 2044
  encoding format: format 2330
output: Sequence
  type: FormalParameter
  additional type: data 2044
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic_0797
application sub category: topic 3308
application sub category: topic 3810
author: https://orcid.org/0000-0003-1849-1269
citation: nature11241
citation: bat035
citation: pmcid:PMC3662865
citation: pubmed:22801500
citation: pubmed:23707967
description: A Next-Generation Information System for Musa genomics
feature list: operation_0338
feature list: operation 2403
feature list: operation 3208
funder: ANR
is accessible for free: true
license: GPL-2.0
software help: 2.x
software help: documentation
software help: termofservices
software version: v2
primary contact: https://orcid.org/0000-0003-1849-1269

Barnaba
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0099
citation: rna.067678.118
citation: pmcid:PMC6348988
citation: pubmed:30420522
description: Software for analysis of nucleic acid structures and trajectories.
feature list: operation_0249
feature list: operation_0279
feature list: operation 2518
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
primary contact: Small RNAs in silico

BasePlayer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0199
application sub category: topic 3325
application sub category: topic 3673
application sub category: topic 3676
author: Riku Katainen
citation: s41596-018-0052-3
citation: https://doi.org/10.1101/126482
citation: pubmed:30323186
description: Large-scale discovery tool for potential causative mutations in human coding and noncoding genome.
feature list: operation 3196
feature list: operation 3211
feature list: operation 3227
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: home.html
primary contact: Riku Katainen

BatMeth2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3674
citation: s12859-018-2593-4
citation: pmcid:PMC6343306
citation: pubmed:30669962
description: Integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping.
feature list: operation 3186
feature list: operation 3206
feature list: operation 3207
is accessible for free: true
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Guoliang Li

BayICE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 2640
application sub category: topic 3308
citation: https://doi.org/10.1101/732743
description: A hierarchical Bayesian deconvolution model with stochastic search variable selection | Bayesian deconvolution model for intracellular component exploration (BayICE)
feature list: operation 3629
license: GPL-3.0

BayesPI-BAR2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0749
application sub category: topic 2640
citation: fgene.2019.00282
citation: pmcid:PMC6454009
citation: pubmed:31001324
description: Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts.
feature list: operation_0477
feature list: operation 3202
is accessible for free: true
operating system: Linux
operating system: Mac
primary contact: Junbai Wang
primary contact: Kirill Batmanov

BayesianPredictiveFutility
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 3379
citation: TCR.2019.05.17
citation: pmcid:PMC6711387
citation: pubmed:31456910
description: Application of Bayesian predictive probability for interim futility analysis in single-arm phase II trial | The tool provides futility interim analysis plan using the Bayesian predictive design in single arm early phase II clinical trial. It also generates statistical plan so clinicians could easily incorporate it into the clinical trial protocol. (reference: Application of Bayesian predictive probability for interim analysis in single-arm early phase II trial. Chen et al; submitted) | devtools::install_github("dungtsa/BayesianPredictiveFutility",force = TRUE) | The shiny applictaion provides futility interim analysis plan for the Bayesian predictive design design in single arm early phase II clinical trial and generates a statistical plan to be easily incorporated into the clinical trial protocol | Simply run the following from an R console:
feature list: operation 3454

Bazam
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
citation: s13059-019-1688-1
citation: pmcid:PMC6472072
citation: pubmed:30999943
description: Method for read extraction and realignment of high-throughput sequencing data.
feature list: operation 3192
feature list: operation 3198
feature list: operation 3227
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Simon Sadedin

BCOOL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0081
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 3168
citation: BTZ548
citation: pubmed:31808510
description: self-correction of short reads via mapping on de Bruijn graphs. de Bruijn graph cOrrectiOn from graph aLignment. Bcool clone and compile Bcalm2 Bgreat2 Btrim and Ntcard
feature list: operation_0524
feature list: operation 3192
feature list: operation 3195
feature list: operation 3198
feature list: operation 3472
license: AGPL-3.0

BeamDelta
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0081
application sub category: topic_0196
application sub category: topic 3068
application sub category: topic 3306
application sub category: topic 3385
citation: WELLCOMEOPENRES.15576.1
description: simple alignment tool for optical systems. BeamDelta is called from the command line using the following format:. A simple GUI interface for python-microscope which allows a compatible camera (see python-microscope compatibility list) to be used for optical alignment purposes. The GUI will display live images, calculate and mark beam centroids and then store an alignment centroid position. Once a position is stored the live centroid then displays a pixel based delta position to allow precise alignment between the marked position and the new beam. We include a suggested parts list in BeamDelta-parts-list.csv which enables the construction of a two camera alignment setup. This hardware configuration will allow both lens alignment and co-aligning two beams and has a small footprint so can relatively easily be mounted within an existing setup
feature list: operation_0292
feature list: operation_0310
feature list: operation 3435
license: GPL-3.0

BeanMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: A mine with common bean data from the Legume Info tripal.chado database
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 0.10

Bellerophon
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0769
application sub category: topic 3170
application sub category: topic 3308
citation: ECE3.5571
citation: pmcid:PMC6787812
citation: pubmed:31624564
description: The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras. Bellerophon is a pipeline created to remove falsely assembled chimeric transcripts in de novo transcriptome assemblies. The pipeline can be downloaded as a vragrant virtual machine (https://app.vagrantup.com/bellerophon/boxes/bellerophon). This is recommended, as it avoids backwards compatibility problems with TransRate
feature list: operation_0450
feature list: operation_0524
feature list: operation 2428
feature list: operation 3258
feature list: operation 3644

Benchmarker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0602
application sub category: topic 3517
citation: J.AJHG.2019.03.027
citation: pmcid:PMC6556976
citation: pubmed:31056107
description: Benchmarking gene and variant prioritization algorithms for GWAS data.
feature list: operation_0488
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Joel N. Hirschhorn
primary contact: Rebecca Fine

BetaSerpentine
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0154
application sub category: topic_0593
application sub category: topic_0611
citation: btx629
citation: pubmed:29444233
description: Program for reconstruction of amyloid structures containing adjacent β-arches.
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.txt
software version: 1.0
primary contact: Andrey V. Kajava
primary contact: Stanislav A. Bondarev

BiAlign
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0099
citation: https://doi.org/10.1101/631606
description: Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure.
feature list: operation_0278
feature list: operation_0491
feature list: operation_0502
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Ivo L. Hofacker
primary contact: Maria Waldl
primary contact: Michael T. Wolfinger
primary contact: Sebastian Will

BiG-SCAPE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0091
application sub category: topic_0102
application sub category: topic_0623
application sub category: topic 3172
application sub category: topic 3697
citation: s41589-019-0400-9
citation: pmcid:PMC6917865
citation: pubmed:31768033
description: A computational framework to explore large-scale biosynthetic diversity. BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity. It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency... BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.
feature list: operation_0303
feature list: operation_0496
feature list: operation 3432

BiGG Models
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3172
application sub category: topic 3293
application sub category: topic 3407
citation: gkz1054
citation: pmcid:PMC7145653
citation: pubmed:31696234
description: BiGG Models is a website for browsing gold-standard genome-scale models, multi-strain genome-scale models and expansion across the phylogenetic tree. BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions.
feature list: operation_0323
feature list: operation_0326
feature list: operation 3660
software help: about
software help: license

BiSpark
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3674
citation: s12859-018-2498-2
citation: pmcid:PMC6288881
citation: pubmed:30526492
description: Spark-based highly scalable aligner for bisulfite sequencing data.
feature list: operation 3186
feature list: operation 3198
feature list: operation 3436
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: BiSpark

BiTSC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3170
application sub category: topic 3474
application sub category: topic 3518
citation: https://doi.org/10.1101/865378
description: Bipartite Tight Spectral Clustering (BiTSC) Algorithm for Identifying Conserved Gene Co-clusters in Two Species. Yidan Eden Sun, Heather J. Zhou and Jingyi Jessica Li. $ python3 BiTSC.py ./data/orthologs_data_uniq.csv ./data/dm_timecourse_FPKMs.csv ./data/ce_timecourse_FPKMs.csv 30 10 100 0.8 10 10 ./data/result 0.90 0.95 1.00
feature list: operation_0313
feature list: operation 2454
feature list: operation 3501

BiWalkLDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 2640
citation: S12859-019-3128-3
citation: pmcid:PMC6876073
citation: pubmed:31760932
description: A novel algorithm based on bi-random walks to identify disease-related lncRNAs. EMAIL: jhu@nwpu.edu.cn, yiqun.gao@nwpu-bioinformatics.com. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. BiWalkLDA.m: BiwalkLDA framework to predict potential lncRNA-disease association. normFun.m: Laplacian normalization
feature list: operation 3435
license: Other

BiasDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic_0209
application sub category: topic 2258
application sub category: topic 3071
application sub category: topic 3336
application sub category: topic 3343
citation: https://doi.org/10.1101/742643
description: A Comprehensive Database for Biased GPCR Ligands | A manually curated database of biased GPCR ligands | BiasDB[1] is a manually curated database containing all published biased GPCR ligands. BiasDB currently contains 615 bias cases of signaling bias representing 481 individual ligands for 61 receptors. We provide information about the chemical structure, target receptor, type of bias, assay categories used for bias determination, reference ligand and literature source. BiasDB is a resource for medicinal chemists, pharmacologists and researchers interested in biased GPCR signaling
feature list: operation_0337
feature list: operation_0482
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

BigStitcher
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3382
application sub category: topic 3500
citation: S41592-019-0501-0
citation: pubmed:31384047
description: Reconstructing high-resolution image datasets of cleared and expanded samples | ImgLib2/BDV implementation of Stitching for large datasets | The BigStitcher is a software package that allows simple and efficient alignment of multi-tile and multi-angle image datasets, for example acquired by lightsheet, widefield or confocal microscopes. The software supports images of almost arbitrary size ranging from very small images up to volumes in the range of many terabytes, which are for example produced when acquiring cleared tissue samples with lightsheet microscopy
feature list: operation_0232
feature list: operation 3552
feature list: operation 3629
license: GPL-2.0

Bigram-PGK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0601
citation: S12860-019-0240-1
citation: pmcid:PMC6923822
citation: pubmed:31856704
description: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix. Phosphoglycerylation prediction using evolutionary information of amino acids. Run the file Bigram_PGK.m to obtain statistical measures of the Bigram_PGK predictor. The algorithm runs on the train and test data to obtain the values. Preprocessing_BigramPGK.m file was used to carry out preprocessing for Bigram_PGK predictor, which includes feature extraction for segment size of ±32, filtering, and construction of train and test sets for 10-fold cross-validation. Everytime the algorithm is executed, it will have a slightly different combination of samples for train and test sets. Nevertheless, the performance will be similar
feature list: operation_0417
feature list: operation 3435
feature list: operation 3755

BinDash
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic 3174
citation: bty651
citation: pubmed:30052763
description: Software for fast genome distance estimation on a typical personal laptop.
feature list: operation 3798
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: XiaoFei Zhao

BindSpace
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3179
citation: S41592-019-0511-Y
citation: pmcid:PMC6717532
citation: pubmed:31406384
description: BindSpace decodes transcription factor binding signals by large-scale sequence embedding | The decoding of transcription factor (TF) binding signals in genomic DNA is a fundamental problem. Here we present a prediction model called BindSpace that learns to embed DNA sequences and TF labels into the same space. By training on binding data from hundreds of TFs and embedding over 1 M DNA sequences, BindSpace achieves state-of-the-art multiclass binding prediction performance, in vitro and in vivo, and can distinguish between signals of closely related TFs
feature list: operation_0420
feature list: operation_0445
feature list: operation 3222

Binner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0091
application sub category: topic_0154
application sub category: topic 3172
citation: btz798
citation: pmcid:PMC7828469
citation: pubmed:31642507
description: Binner is a Java application for deep annotation of untargeted LC-MS metabolomics data. It takes a numerical feature table obtained from any preprocessing software (e.g. XCMS, MZmine) as input and outputs a file with clusters of closely eluting, highly correlated metabolite features that are most related, along with their pairwise correlations, mass differences, and putative annotations.
feature list: operation 3432

Bio-DIA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 2258
application sub category: topic 3372
citation: https://doi.org/10.1101/2019.12.13.875666
description: A web-based tool for data and algorithms integration.
feature list: operation 2422

Bio2BEL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic 2258
citation: https://doi.org/10.1101/631812
description: Integration of Structured Biological Data Sources using Biological Expression Language.
feature list: operation_0533
feature list: operation 1812
feature list: operation 3501
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest
primary contact: Charles Tapley Hoyt

BioBERT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic 3303
citation: btz682
citation: pmcid:PMC7703786
citation: pubmed:31501885
description: A pre-trained biomedical language representation model for biomedical text mining | BioBERT: a pre-trained biomedical language representation model | This repository provides pre-trained weights of BioBERT, a language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. Please refer to our paper BioBERT: a pre-trained biomedical language representation model for biomedical text mining for more details | This repository provides fine-tuning codes of BioBERT, a language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. Please refer to our paper BioBERT: a pre-trained biomedical language representation model for biomedical text mining for more details. This project is done by DMIS-Lab
feature list: operation 3280
feature list: operation 3625

BioCell2XML
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
application sub category: topic 3382
citation: S00427-019-00633-9
citation: pubmed:31119364
description: Tool for converting cell lineage data from SIMI BioCell to MaMuT (Fiji).
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: BioCell2XML User Guide.pdf
primary contact: Carsten Wolff
primary contact: Günther Loose
primary contact: Markus Pennerstorfer

BioEn
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic_0593
application sub category: topic 3474
citation: CHEMRXIV.7461413.V2
description: Efficient Ensemble Refinement by Reweighting. BioEn - Bayesian Inference Of ENsembles. BioEn integrates a broad range of experimental data to refine ensembles of structures. For a detailed description of the procedures and the algorithm, we refer to [Hummer2015]
feature list: operation_0337
feature list: operation 2425
feature list: operation 2476
feature list: operation 3799
feature list: operation 3891

BioEra
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3315
application sub category: topic 3382
description: Visual designer for biofeedback. Provides environment and tools to create various types of processing tasks.
feature list: operation_0337
is accessible for free: true
license: GPL-3.0
operating system: Windows
software help: manual.html

BioExplorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3334
description: Program for real-time biophysical data acquisition, processing, and display.
is accessible for free: false
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.7

BioFabric
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0081
application sub category: topic_0602
application sub category: topic 3474
application sub category: topic 3500
citation: https://doi.org/10.1101/2019.12.18.881664
description: BioFabric is an open-source network visualization tool.
feature list: operation_0491
feature list: operation_0496
feature list: operation 3083

BioGRID Open Repository of CRISPR Screens (ORCS)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 3053
citation: gky1079
citation: pmcid:PMC6324058
citation: pubmed:30476227
description: BioGRID ORCS is an open repository of CRISPR screens compiled through comprehensive curation efforts. Our current index searches more than 49 publications and 58,161 genes to return more than 895 CRISPR screens from 3 major model organism species and 629 cell lines.All screen data are freely provided through our search index and available via download in a wide variety of standardized formats.
feature list: operation_0224
feature list: operation 1777
feature list: operation 1781
feature list: operation 3439
is accessible for free: true
software help: ORCS
software version: 1.0

BioGateway
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: SPARQL endpoint
application sub category: topic_0089
application sub category: topic_0128
citation: BTZ835
citation: pmcid:PMC7703768
citation: pubmed:31710663
description: A triple store with RDF graphs obtained from various curated databases, queryable by SPARQL and through the Cytoscape plugin BioGateway App.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: advanced queries
software help: example tutorial
software version: 3.0

BioGears Engine
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 3300
application sub category: topic 3314
application sub category: topic 3315
application sub category: topic 3407
citation: FPHYS.2019.01321
citation: pmcid:PMC6813930
citation: pubmed:31681022
description: BioGears® is a open source, comprehensive human physiology engine that will drive medical education, research, and training technologies.
feature list: operation_0337
feature list: operation 2426
feature list: operation 3454
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows

BioMedR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic 2258
application sub category: topic 3168
application sub category: topic 3336
citation: BBZ150
citation: pubmed:31885044
description: an R/CRAN package for integrated data analysis pipeline in biomedical study. generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions. The BioMedR package offers an R package for generating various molecular descriptors for chemicals, proteins, DNAs RNAs and their interactions. Calculating 293 chemical descriptors and 14 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 DNA/RNA descriptors from nucleotide sequences, and six types of interaction descriptors using three different combining strategies
feature list: operation_0262
feature list: operation 2929
feature list: operation 3894
license: GPL-2.0

BioMercator
type: SoftwareApplication
input: Genome map
  type: FormalParameter
  additional type: data 1288
  encoding format: format 1975
input: QTL map
  type: FormalParameter
  additional type: data 1860
  encoding format: format 2330
  encoding format: format 2332
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0780
application sub category: topic 3055
citation: bth230
citation: pubmed:15059820
description: BioMercator is a software that provides a complete set of algorithms and visualization tool covering all steps required to perform QTL meta-analysis, graphical representation of large datasets. User may import sequence and genome annotations datasets within the software in order to display functional annotation related to QTL and meta-QTL.
feature list: operation_0282
feature list: operation 2944
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 4.2.3

BioMethyl
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 3295
application sub category: topic 3518
citation: btz137
citation: pmcid:PMC6761945
citation: pubmed:30799505
description: R package for Biological interpretation of DNA methylation data in the TCGA cancers context.
feature list: operation_0533
feature list: operation 3207
feature list: operation 3501
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Chao Cheng
primary contact: Yue Wang

BioMine-DB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0078
application sub category: topic_0084
application sub category: topic_0154
application sub category: topic_0621
citation: PEERJ.PREPRINTS.1983V2
description: A database for metazoan biomineralization proteins. Biomineralization is the process by which living organisms construct hard skeletons creating complex structures that range from specialized tissues such as bone or teeth to ecosystems such as coral reefs. Biominerals are composed of both inorganic minerals and proteins, which give them extra hardness and special attributes. Biomineralization proteins are also known to be associated with multiple bone disorders and are therefore of biomedical importance. Herein we describe BioMine-DB, a biomineralization centric protein database. Availability and implementation: BioMine-DB can be accessed at http: biomine.net, SQL dump, FASTA files and source code are available for download as well at https: github.com bishoyh biomineDB "

BioNet-Mining
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic_0769
application sub category: topic 2259
application sub category: topic 3473
citation: PEERJ.PREPRINTS.1479V3
citation: PEERJ.PREPRINTS.1479V4
description: The biological network mining workflow identifies frequent structural patterns in biochemical reaction networks encoded in the Systems Biology Markup Language (SBML). The repository contains the scripts for a workflow that identifies frequent structural patterns in biochemical reaction networks encoded in the Systems Biology Markup Language.
feature list: operation_0239
feature list: operation 2422
feature list: operation 3660

BioNix
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0091
application sub category: topic_0769
description: Bioinformatics workflows in the functional Nix language
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
primary contact: Mailing list

BioStructMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Web application
additional type: Web service
application sub category: topic_0166
application sub category: topic_0736
application sub category: topic 2830
citation: bty474
description: Python tool for integration of protein structure and sequence-based features.
feature list: operation_0302
feature list: operation 3436
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
software help: biostructmap
primary contact: Andrew Guy
primary contact: Dr. Paul Ramsland

BioSwitch
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3070
citation: BTZ746
citation: pubmed:31609384
description: A tool for the detection of bistability and multi-steady state behaviour in signaling and gene regulatory networks. https://sites.google.com/view/bioswitch. BioSwitch is a Matlab software tool for detection of multi-steady state behaviour in biochemical reaction networks (specially suited for signaling and gene regulatory networks)
feature list: operation 2497
feature list: operation 3799

Biobtree
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 3489
application sub category: topic 3500
citation: F1000RESEARCH.17927.2
description: A tool to search and map bioinformatics identifiers and special keywords | A bioinformatics tool to search and map identifiers and special keywords | Biobtree is a bioinformatics tool which process large datasets effectively and provide uniform search and mapping functionalities with web interface and web services for genomic research
feature list: operation 2422
license: BSD-3-Clause

BiocPkgTools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0091
application sub category: topic_0218
application sub category: topic 3473
citation: f1000research.19410.1
citation: pmcid:PMC6584971
citation: pubmed:31249680
description: Package that facilitates access to extensive metadata in computable form covering the Bioconductor package ecosystem, facilitating downstream applications such as custom reporting, data and text mining of Bioconductor package text descriptions, graph analytics over package dependencies, and custom search approaches.
feature list: operation_0306
feature list: operation_0337
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Sean Davis

BiofilmQ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3382
application sub category: topic 3697
application sub category: topic 3810
citation: https://doi.org/10.1101/735423
description: A software tool for quantitative image analysis of microbial biofilm communities | Software tool for quantitative analysis of microbial biofilm images | Developed by Raimo Hartmann, Hannah Jeckel, Eric Jelli, Knut Drescher | Analysis supports any biofilm type
feature list: operation 3196
feature list: operation 3552
feature list: operation 3799

Bioinformatics Docker Images Project
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
additional type: Suite
additional type: Workflow
application sub category: topic_0080
application sub category: topic_0092
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3293
author: https://orcid.org/0000-0002-4657-6991
author: https://orcid.org/0000-0002-6476-7206
author: https://orcid.org/0000-0002-7139-2107
description: A collection of 40+ well-documented Docker images of commonly used bioinformatics applications and pipelines.
feature list: operation_0292
feature list: operation_0324
feature list: operation 2403
feature list: operation 2409
is accessible for free: true
operating system: Linux
operating system: Windows
primary contact: https://orcid.org/0000-0001-7032-5220

BiomeNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0621
application sub category: topic_0780
application sub category: topic 3174
application sub category: topic 3500
citation: btz776
citation: pmcid:PMC7703761
citation: pubmed:31599923
description: A database for construction and analysis of functional interaction networks for any species with a sequenced genome. Earth BioGenome Project has been officially launched in November 2018 with the goal of decoding genomes of Earth’s biome over a period of 10 years. For every sequenced species, genome annotation will be followed by functional annotation for individual genes and pathways. Network biology can facilitate functional annotations of genomes in the context of collaborative interactions between genes. BiomeNet is a database of scored functional networks enabling network biology for every sequenced genome of Earth’s biome. With protein sequences of target species submitted by users, BiomeNet will transfer co-functional links between orthologous proteins from 95 source networks (comprising ~8 million links), which were previously constructed and validated for 18 species (5 animals, 6 plants, 5 bacteria, and 2 fungi)
feature list: operation_0277
feature list: operation_0525
feature list: operation 3439
feature list: operation 3672

Biome-Shiny
type: SoftwareApplication
input: Database search results
  type: FormalParameter
  additional type: data 2080
  encoding format: format 3746
output: Plot
  type: FormalParameter
  additional type: data 2884
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3174
description: A Shiny R app for microbiome visualization, built around the "microbiome" package.
feature list: operation_0337
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software version: 0.9

Biomine Explorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
author: Vid Podpečan
citation: btz509
citation: pmcid:PMC6954666
citation: pubmed:31233141
contributor: Hannu Toivonen
contributor: Kristina Gruden
contributor: Nada Lavrač
contributor: Živa Ramšak
description: Biomine Explorer is a web application that enables interactive exploration of selected publicly available biological knowledge. It is based on the results of the Biomine project that develops methods for the analysis of public biological data sources (annotated sequences, proteins, domains, and orthology groups, genes and gene expressions, gene and protein interactions, scientific articles, and ontologies). All information is handled as networks and Biomine provides probabilistic network search algorithms to automatically extract the most relevant subnetworks. The most prominent feature of Biomine Explorer is interactive exploration of its large probabilistic networks by using an interactive network visualisation interface. Network editing features and private network repositories are also available as well as a repository of publicly available graphs. All links to Biomine graphs are permanent so they can be used in scientific publications or published on the web.
feature list: operation_0337
feature list: operation 3927
provider: Jožef Stefan Institute, Department of Knowledge Technologies
software help: biomine.ijs.si
primary contact: Vid Podpečan

Bionitio
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0102
citation: GIZ109
citation: pmcid:PMC6755254
citation: pubmed:31544213
description: Demonstrating and facilitating best practices for bioinformatics command-line software | Demonstrating best practices for bioinformatics command line tools | Bionitio provides a template for command line bioinformatics tools in various programming languages | The purpose of the tool is to provide an easy-to-understand working example that is built on best-practice software engineering principles. It can be used as a basis for learning and as a solid foundation for starting new projects. We provide a script called bionitio-boot.sh for starting new projects from bionitio, which saves time and ensures good programming practices are adopted from the beginning (see below for details)
feature list: operation 3435
license: MIT

BitEpi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3518
citation: https://doi.org/10.1101/858282
description: A Fast and Accurate Exhaustive Higher-Order Epistasis Search. BitEpi: An exhaustive search of higher-order epistatic interactions. BitEpi is software for an exhaustive search of higher-order epistatic interactions between genomic variants (SNPs) given a binary phenotype (Case/Control). BitEpi performs an exhaustive search that means it tests all possible combinations of SNPs. For example, the 4-SNP search of 50 SNPs (data.csv) requires to test all "4 out of 50" 4-SNP combinations (230300 4-SNP combinations)
feature list: operation_0337
feature list: operation 2421
feature list: operation 3196

BitterSweet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3474
application sub category: topic 3855
citation: S41598-019-43664-Y
citation: pmcid:PMC6509165
citation: pubmed:31073241
description: Building machine learning models for predicting the bitter and sweet taste of small molecules.
feature list: operation 3216
feature list: operation 3280
feature list: operation 3891
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: faq
software help: how to use
primary contact: https://orcid.org/0000-0003-1924-6070

BlackSheep
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3325
citation: ACS.JPROTEOME.1C00190
citation: pmcid:PMC8256816
citation: pubmed:34165986
description: A Bioconductor and Bioconda package for differential extreme value analysis. A tool for differential extreme-value analysis. Differential extreme outlier analysis using Blacksheep. https://blacksheep.readthedocs.io/en/master/. conda install -c bioconda blksheep. Requirements (automatically taken care of with pip and conda)
feature list: operation_0337
feature list: operation 2238
feature list: operation 2495
feature list: operation 3223
feature list: operation 3436
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: master

BlobToolKit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0194
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic_0769
application sub category: topic 3050
application sub category: topic 3500
citation: https://doi.org/10.1101/844852
citation: g3.119.400908
citation: pmcid:PMC7144090
citation: pubmed:32071071
description: BlobToolKit Viewer is a genome-scale dataset visualistion tool developed as part of the blobtoolkit project to allow browser-based identification and filtering of target and non-target data in genome assemblies.
feature list: operation_0337
feature list: operation_0525
feature list: operation 1812
feature list: operation 3216
feature list: operation 3431
license: MIT

Bolt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: S13361-019-02306-3
citation: pubmed:31452088
description: A cloud-based peptide search engine for MS/MS sequencing.
feature list: operation 2929
feature list: operation 3645
feature list: operation 3646
is accessible for free: false
license: Proprietary

BovineMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: An integrated data warehouse for the Bovine Genome Database
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 1.4

BowSaw
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3174
application sub category: topic 3474
application sub category: topic 3697
citation: https://doi.org/10.1101/839357
description: A random forest model for inferring higher-order trait interactions associated with complex biological phenotypes.
feature list: operation 2495
feature list: operation 3659

BrainBay
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3334
description: Bio and Neurofeedback Application, designed to work with various Electroencephalography (EEG) amplifiers. It supports Human-Computer-Interface functions and NeuroServer Software Framework to transmit live recordings via Internet or LAN.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: docu.htm
software help: BrainBay
software version: 2.4
primary contact: Chris Veigl

BrainSpace
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3334
application sub category: topic 3384
citation: s42003-020-0794-7
citation: https://doi.org/10.1101/761460
citation: pmcid:PMC7058611
citation: pubmed:32139786
description: a toolbox for the analysis of macroscale gradients in neuroimaging and connectomics datasets | BrainSpace is an open-access toolbox that allows for the identification and analysis of gradients from neuroimaging and connectomics datasets : available in both Python and Matlab : | Welcome to BrainSpace’s documentation! — BrainSpace 0.1.0 documentation | Free document hosting provided by Read the Docs
feature list: operation 3891
license: BSD-3-Clause
software help: brainspace.readthedocs.io

Brain Interactome Explorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3304
citation: J.ISCI.2019.10.026
citation: pmcid:PMC6838536
citation: pubmed:31677479
description: Systematic Identification of Cell-Cell Communication Networks in the Developing Brain. Since the generation of cell-type specific knockout models, the importance of inter-cellular communication between neural, vascular, and microglial cells during neural development has been increasingly appreciated. However, the extent of communication between these major cell populations remains to be systematically mapped. Here, we describe EMBRACE (embryonic brain cell extraction using FACS), a method to simultaneously isolate neural, mural, endothelial, and microglial cells to more than 94% purity in ∼4 h. Utilizing EMBRACE we isolate, transcriptionally analyze, and build a cell-cell communication map of the developing mouse brain. We identify 1,710 unique ligand-receptor interactions between neural, endothelial, mural, and microglial cells in silico and experimentally confirm the APOE-LDLR, APOE-LRP1, VTN-KDR, and LAMA4-ITGB1 interactions in the E14.5 brain
feature list: operation 2429
feature list: operation 3446

Branch
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3334
application sub category: topic 3399
application sub category: topic 3408
citation: btw117
description: Interactive, web-based tool for testing hypotheses and developing predictive models.
feature list: operation 3359
feature list: operation 3431
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Andrew I. Su
primary contact: Benjamin M. Good

Broccoli
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0769
application sub category: topic 3293
application sub category: topic 3474
citation: msaa159
citation: https://doi.org/10.1101/2019.12.13.875831
citation: pubmed:32602888
description: combining phylogenetic and network analyses for orthology assignment. orthology assignment using phylogenetic and network analyses. Broccoli, a user-friendly pipeline designed to infer with high precision orthologous groups and pairs of proteins using a phylogeny-based approach. Briefly, Broccoli performs ultra-fast phylogenetic analyses on most proteins and builds a network of orthologous relationships. Orthologous groups are then identified from the network using a parameter-free machine learning algorithm (label propagation). Broccoli is also able to detect chimeric proteins resulting from gene-fusion events and to assign these proteins to the corresponding orthologous groups
feature list: operation_0327
feature list: operation 3432
license: GPL-3.0

C-I-TASSER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0736
application sub category: topic_0749
citation: PROT.25792
citation: pmcid:PMC6851476
citation: pubmed:31365149
description: Deep-learning contact-map guided protein structure prediction in CASP13 | contact-guided protein structure prediction | C-I-TASSER (Contact-guided Iterative Threading ASSEmbly Refinement) is a composite approach that uses contact information to enhance the accuracy of protein structure and function predictions | [View example output] [Check previous jobs] [Server statistics] [Help] [Forum]
feature list: operation_0272
feature list: operation_0476
feature list: operation 3350

C-InterSecture
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0102
application sub category: topic 3292
citation: btz415
citation: pubmed:31116383
description: C-InterSecture (Computional tool for InterSpecies analysis of genome architecture) - pipeline to cross-species comparison of Hi-C map. C-InterSecture was designed to liftover contacts between species, compare 3-dimensional organization of defined genomic regions, such as TADs, and analyze statistically individual contact frequencies.
feature list: operation 3501
feature list: operation 3798
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: ReadMe.md
primary contact: M. Nuriddinov

C-JAMP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 3170
application sub category: topic 3517
citation: GEPI.22265
citation: pubmed:31732979
description: Powerful rare variant association testing in a copula-based joint analysis of multiple phenotypes. Copula-Based Joint Analysis of Multiple Phenotypes. We provide a computationally efficient and robust implementation of the recently proposed C-JAMP (Copula-based Joint Analysis of Multiple Phenotypes) method (Konigorski et al., 2019, submitted)
feature list: operation 3196
feature list: operation 3659
feature list: operation 3791
license: GPL-2.0

Consensus Cancer driver gene Caller (C3)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3168
citation: J.GPB.2018.10.004
citation: pmcid:PMC6818389
citation: pubmed:31465854
description: Consensus Cancer Driver Gene Caller | Next-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells. A key challenge in interpreting cancer genomes is to distinguish drivers of cancer development among available genetic mutations. To address this issue, we present the first web-based application, consensus cancer driver gene caller (C3), to identify the consensus driver genes using six different complementary strategies, i.e., frequency-based, machine learning-based, functional bias-based, clustering-based, statistics model-based, and network-based strategies. This application allows users to specify customized operations when calling driver genes, and provides solid statistical evaluations and interpretable visualizations on the integration results

C3D
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3168
application sub category: topic 3173
citation: bty717
citation: pubmed:30816925
description: Cross Cell-type Correlation in DNaseI hypersensitivity (C3D) - tool to predict 3D genomic interactions between cis-regulatory elements.
feature list: operation_0441
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Tahmid Mehdi

CABS-dock
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 3336
application sub category: topic 3957
citation: PRO.3771
citation: TMI.13348
citation: pmcid:PMC6933849
citation: pubmed:31682301
citation: pubmed:31733137
description: A web application for flexible protein-peptide docking.
feature list: operation_0480
feature list: operation_0482
feature list: operation 2575
feature list: operation 3631
feature list: operation 3899

CADOES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3067
application sub category: topic 3474
citation: J.FORSCIINT.2019.109873
citation: pubmed:31382223
description: An interactive machine-learning approach for sex estimation with the pelvis | The pelvis is consistently regarded as the most sexually dimorphic region of the human skeleton, and methods for sex estimation with the pelvic bones are usually very accurate. In this investigation, population-specific osteometric models for the assessment of sex with the pelvis were designed using a dataset provided by J. A. Serra (1938) that included 256 individuals (131 females and 125 males) from the Coimbra Identified Skeletal Collection and 38 metric variables. The models for sex estimation were operationalized through an online application and decision support system, CADOES. Different classification algorithms generated high accuracy models, ranging from 85% to 92%, with only three variables; and from 85.33% to 97.33%, with all 38 variables

CALIMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3382
citation: J.CMPB.2019.104991
citation: pmcid:PMC6718774
citation: pubmed:31443860
description: The semi-automated open-source calcium imaging analyzer | CalciumImagingAnalyser is free software for the extraction and analysis of calcium imaging footage. Designed to be fast, user-friendly and portable, it includes such functions as spatiotemporal and network analysis | CALciumIMagingAnalyser (CALIMA) is a free application for the extraction and analysis of calcium imaging data. Read more below or go straight to the download section
feature list: operation 3450
feature list: operation 3660

CAM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0194
application sub category: topic_0637
citation: PEERJ.PREPRINTS.27756
description: Codon Aversion Motifs for Alignment-free Phylogenies.
feature list: operation_0284
feature list: operation 2962
feature list: operation 2964
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README
primary contact: Justin Miller

Community Assembly Model Inference (CAMI)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0196
application sub category: topic_0610
application sub category: topic_0625
application sub category: topic 2269
citation: ECE3.5773
citation: pmcid:PMC6912896
citation: pubmed:31871640
description: Identifying models of trait-mediated community assembly using random forests and approximate Bayesian computation. Community Assembly Model Inference. For full Installation instructions and initial uses, refer to vignette ‘CAMI_Installation.Rmd’. Briefly, you can install the R package using devtools::install_github("ruffleymr/CAMI")
feature list: operation_0310
feature list: operation 2426
feature list: operation 3659
feature list: operation 3695

CAMISIM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: s40168-019-0633-6
citation: pmcid:PMC6368784
citation: pubmed:30736849
description: Software to model abundance distributions of microbial communities and to simulate corresponding shotgun metagenome datasets.
feature list: operation_0310
feature list: operation 3460
feature list: operation 3798
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: User-manual

CAMND
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3407
citation: J.BIOSYSTEMS.2019.104081
citation: pubmed:31838143
description: Comparative analysis of metabolic network decomposition based on previous and two new criteria. Metabolic networks can model the behavior of metabolism in the cell. Since analyzing the whole metabolic networks is not easy, network modulation is an important issue to be investigated. Decomposing metabolic networks is a strategy to obtain better insight into metabolic functions. Additionally, decomposing these networks facilitates using computational methods, which are very slow when applied to the original genome-scale network. Several methods have been proposed for decomposing of the metabolic network. Therefore, it is necessary to evaluate these methods by suitable criteria.
feature list: operation_0337
feature list: operation 3660

CANDI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0634
application sub category: topic 3384
application sub category: topic 3474
citation: bty855
citation: pmcid:PMC6499410
citation: pubmed:30304439
description: R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis.
feature list: operation_0337
feature list: operation 3553
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: candi
primary contact: M. A. Badgeley

Computational Analysis of Novel Drug Opportunities (CANDO)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic 2275
application sub category: topic 3336
application sub category: topic 3379
citation: acs.jcim.0c00110
citation: https://doi.org/10.1101/845545
citation: pmcid:PMC8098009
citation: pubmed:32515949
description: CANDO is a open-source, unique computational drug discovery, design, and repurposing platform.
feature list: operation_0477
feature list: operation_0478
feature list: operation 2575
license: BSD-3-Clause

CANet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3063
citation: TMI.2019.2951844
citation: pubmed:31714219
description: Cross-disease Attention Network for Joint Diabetic Retinopathy and Diabetic Macular Edema Grading. Diabetic retinopathy (DR) and diabetic macular edema (DME) are the leading causes of permanent blindness in the working-age population. Automatic grading of DR and DME helps ophthalmologists design tailored treatments to patients, thus is of vital importance in the clinical practice. However, prior works either grade DR or DME, and ignore the correlation between DR and its complication, i.e., DME. Moreover, the location information, e.g., macula and soft hard exhaust annotations, are widely used as a prior for grading. Such annotations are costly to obtain, hence it is desirable to develop automatic grading methods with only image-level supervision. In this paper, we present a novel cross-disease attention network (CANet) to jointly grade DR and DME by exploring the internal relationship between the diseases with only image-level supervision
feature list: operation 3659

CAPICE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3320
application sub category: topic 3384
application sub category: topic 3474
application sub category: topic 3676
citation: https://doi.org/10.1101/19012229
citation: s13073-020-00775-w
citation: pmcid:PMC7446154
citation: pubmed:32831124
description: A computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations.
feature list: operation 3225
feature list: operation 3226
feature list: operation 3461

The Comprehensive Antibiotic Resistance Database (CARD)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0089
application sub category: topic 2885
application sub category: topic 3174
application sub category: topic 3305
application sub category: topic 3673
citation: gkz935
citation: pmcid:PMC7145624
citation: pubmed:31665441
description: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database.
feature list: operation_0362
feature list: operation 2421
feature list: operation 3196
feature list: operation 3461
feature list: operation 3482
software help: about

CARNIVAL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic_0749
application sub category: topic 3308
application sub category: topic 3422
citation: S41540-019-0118-Z
citation: pmcid:PMC6848167
citation: pubmed:31728204
description: contextualizing large signaling networks with CARNIVAL. CAusal Reasoning for Network Identification with integer VALue programming in R. CARNIVAL is an R-package providing a framework to perform causal reasoning to infer a subset of signalling network from transcriptomics data. This work was originally based on Melas et al. with a number improved functionalities comparing to the original version. Transcription factors’ (TFs) activities and pathway scores from gene expressions can be inferred with our in-house tools DoRothEA & PROGENy, respectively. TFs’ activities and signed directed protein-protein interaction networks +/- drug targets and pathway scores are then used to derive a series of linear constraints to generate integer linear programming (ILP) problems. An ILP solver (CPLEX) is subsequently applied to identify the sub-network topology with minimised discrepancies on fitting error and model size
feature list: operation_0277
feature list: operation 2436
feature list: operation 3439

Colored Abstract Simplicial Complex (CASC)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3292
application sub category: topic 3315
application sub category: topic 3452
citation: https://doi.org/10.1145/3321515
citation: pmcid:PMC6716611
citation: pubmed:31474782
description: The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation | Colored Abstract Simplicial Complex Library | Colored Abstract Simplicial Complex (CASC) Library | CASC is a modern and header-only C++ library which provides a data structure to represent arbitrary dimension abstract simplicial complexes with user-defined classes stored directly on the simplices at each dimension. This is achieved by taking advantage of the combinatorial nature of simplicial complexes and new C++ code features such as: variadic templates and automatic function return type deduction. Essentially CASC stores the full topology of the complex according to a Hasse diagram. The representation of the topology is decoupled from interactions of user data through the use of metatemplate programming
license: LGPL-2.1

CASet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0199
application sub category: topic 2640
citation: BTZ869
citation: pmcid:PMC7141873
citation: pubmed:31750900
description: Distance Measures for Tumor Evolutionary Trees. MOTIVATION:There has been recent increased interest in using algorithmic methods to infer the evolutionary tree underlying the developmental history of a tumor. Quantitative measures that compare such trees are vital to a number of different applications including benchmarking tree inference methods and evaluating common inheritance patterns across patients. However, few appropriate distance measures exist, and those that do have low resolution for differentiating trees or do not fully account for the complex relationship between tree topology and the inheritance of the mutations labeling that topology.
feature list: operation_0326
feature list: operation_0540
feature list: operation_0557
feature list: operation 3799

Cosolvent Analysis Toolkit (CAT)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic_0749
citation: S41598-019-55394-2
citation: pmcid:PMC6910964
citation: pubmed:31836830
description: A robust hotspot identification platform for cosolvent simulations of proteins to expand the druggable proteome. Cosolvent Analysis Toolkit (CAT). Authors: Frances Sabanes Zariquiey, Joao V. de Souza, Agnieszka K. Bronowska.
feature list: operation_0337
feature list: operation 2476
feature list: operation 2492
feature list: operation 2575
feature list: operation 3891
license: LGPL-3.0

CATANA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3320
application sub category: topic 3512
author: Cheng-Kai Shiau
citation: bty795
description: Tool for generating comprehensive annotations of alternative transcript events.
feature list: operation_0264
feature list: operation 1812
feature list: operation 3800
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
software version: 1.0

CATHER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0102
citation: BTZ876
citation: pubmed:31790141
description: A novel threading algorithm with predicted contacts. CATHER is a threading algorithm for template-based modeling. It uses an iterative algorithm to combine both sequential information and contact maps to improve the threading performance. For a submitted query protein sequence, the returned results include the predicted structure
feature list: operation_0272
feature list: operation_0302
feature list: operation_0474

CATT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 2830
application sub category: topic 3170
citation: btaa432
citation: https://doi.org/10.1101/740340
citation: pubmed:32399561
description: An ultrasensitive T-cell receptor detection method for TCR-Seq and RNA-Seq data | An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data | HomePage: http://bioinfo.life.hust.edu.cn/CATT | An ultra-sensitive and accurate tool for characterizing T cell receptor sequence in bulk and single cell TCR-Seq and RNA-Seq data. The tool can be found in: | CATT(CharActerzing TCR repertoires) is a tool for detecting CDR3 sequences from any TCR containing raw sequencing data (including TCR-seq, RNA-seq, scRNA-seq and any TCR contained sequencing data)
feature list: operation 3192

CAUSALdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3517
citation: gkz1026
citation: pmcid:PMC7145620
citation: pubmed:31691819
description: A database for disease/trait causal variants identified using summary statistics of genome-wide association studies. A GWAS fine-mapping pipeline used in CAUSALdb. CAUSALdb integrates large numbers of GWAS summary statistics and identifies credible sets of causality by uniformly processed fine-mapping
feature list: operation 3196
feature list: operation 3226
feature list: operation 3791

CBGT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3474
citation: JOURNAL.PCBI.1006998
citation: pmcid:PMC6534331
citation: pubmed:31060045
description: Spiking Neural Network of cortico-basal ganglia-thalamus (CBGT) pathways.
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
software help: README.md
primary contact: https://orcid.org/0000-0002-1513-1551
primary contact: https://orcid.org/0000-0003-4720-0336

CBNA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 2640
citation: JOURNAL.PCBI.1007538
citation: pmcid:PMC6907873
citation: pubmed:31790386
description: Controllability based Biological Network Analysis (CBNA) is a tool to uncover coding and non-coding cancer drivers (i.e. miRNA cancer drivers).
feature list: operation_0463
feature list: operation 3202
feature list: operation 3792

CCBGpipe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0654
application sub category: topic 3673
citation: FMICB.2019.02068
citation: pmcid:PMC6737777
citation: pubmed:31551994
description: Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding | A pipeline for completing circular bacterial genomes using a sampling strategy | Since CCBGpipe implements many analytical tools, we strongly recommend you to run it with Docker. Alternatively, you can install all dependencies as listed in the Installation section | This pipeline is designed to complete circular bacterial genomes using a sampling strategy from a sinlge MinION with barcoding
feature list: operation_0525
feature list: operation 3192
feature list: operation 3644
license: GPL-3.0

CCC-Tool
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0632
application sub category: topic 3315
application sub category: topic 3382
citation: TVCG.2019.2961674
citation: pubmed:31870986
description: CCC-Tool (Charting Continuous Colormaps) is a tool for creating, editing, and analyzing such application-specific colormaps.
feature list: operation_0337
feature list: operation 3096
feature list: operation 3435

Cancer Cell Line Authentication (CCLA)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3518
citation: bbaa093
citation: https://doi.org/10.1101/858456
citation: pubmed:32510568
description: an accurate method and web server for cancer cell line authentication using gene expression profiles. Abstract Cancer cell lines (CCLs) as important model systems play critical roles in cancer researches. The misidentification and contamination of CCLs are serious problems, leading to unreliable results and waste of resources. Current methods for CCL authentication are mainly based on the CCL-specific genetic polymorphisms, whereas no method is available for CCL authentication using gene expression profiles. Here, we developed a novel method and homonymic web server (CCLA, Cancer Cell Line Authentication, http: bioinfo.life.hust.edu.cn web CCLA ) to authenticate 1,291 human CCLs of 28 tissues using gene expression profiles. CCLA curated CCL-specific gene signatures and employed machine learning methods to measure overall similarities and distances between the query sample and each reference CCL
feature list: operation_0224
feature list: operation 2495
feature list: operation 3227

CCMP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3360
application sub category: topic 3697
citation: J.YJBINX.2019.100040
citation: pmcid:PMC6719681
citation: pubmed:31482150
description: Software-as-a-service approach for fully-automated microbiome profiling | Microbiome profiling holds great promise for the development of novel disease biomarkers and therapeutics. Next-generation sequencing is currently the preferred method for microbiome data collection and multiple standardized tools, packages, and pipelines have been developed for the purpose of raw data processing and microbial annotation. However, these currently available pipelines come with entry-level barriers such as high-performance hardware, software installation, and sequential command-line scripting that often deter end-users. We thus created Cloud Computing for Microbiome Profiling (CCMP, https: ccmp.usc.edu), a public cloud-based web tool which combines the analytical power of current microbiome analysis platforms with a user-friendly interface

CCMetagen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
additional type: Web service
application sub category: topic 3174
application sub category: topic 3308
application sub category: topic 3697
citation: https://doi.org/10.1101/641332
description: Pipeline to classify organisms in metagenomes or metatranscriptomes accurately.
feature list: operation 3460
feature list: operation 3472
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial
primary contact: Vanessa R. Marcelino

CCSeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0621
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3169
citation: https://doi.org/10.1101/818385
description: Clusters of Colocalized Sequences. Abstract 0.1 Motivation Potential transcription factor (TF) complexes may be identified by testing whether the binding sequences of individual TF proteins form clusters with each other. These clusters may also indicate TF inhibition due to competitive occupancy of enhancer regions. Genome annotation data containing the coordinates of enhancer sequences is highly accessible via position-weight matrix tools. 0.2 Results An algorithm called CCSeq (Clusters of Colocalized Sequences) was developed for identifying clusters of sequences along a one-dimensional line, such as a chromosome, given genome annotation files and a cut-off distance as inputs.
feature list: operation_0291
feature list: operation_0362
feature list: operation 3695

CDAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0637
citation: S41598-019-49225-7
citation: pmcid:PMC6726630
citation: pubmed:31485005
description: An Online Package for Evaluation of Complex Detection Methods | Complex Detection Analyzer Package (CADP) helps you to execute protein complex detection methods and compare their results in a quick and compact ways. It computes a wide range of evaluation criteria and visualize the comparison of methods in tables and multiplots. It assists you in filtering detected clusters by providing a protein name (STRING ID) as a query and by setting constraint on maximum and minimum number of proteins in detected clusters. The list of methods for detecting protein complexes is as follows: | You may look for the values of evaluation criteria for a specific threshold. This can also be done by CDAP. The PPI datasets are: | You can also upload the result of any other method for evaluating its results. The valid format for uploaded file is described here | The list of evaluation criteria is as follows:
feature list: operation 2492
feature list: operation 3501

CDE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3334
application sub category: topic 3379
application sub category: topic 3401
citation: S12028-019-00723-6
citation: S12028-019-00727-2
citation: pubmed:31077078
citation: pubmed:31087257
description: Common Data Elements for Unruptured Intracranial Aneurysm and Subarachnoid Hemorrhage Clinical Research.
feature list: operation 3760
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

Clinical Drug Experience Knowledgebase (CDEK)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3336
application sub category: topic 3373
application sub category: topic 3379
citation: BAZ087
citation: pmcid:PMC6693031
citation: pubmed:31411687
description: Clinical Drug Experience Knowledgebase | Washington University in St. Louis | The Clinical Drug Experience Knowledgebase (CDEK) is a platform intended to explore every active pharmaceutical ingredient (API) with evidence of clinical testing | The Clinical Drug Experience Knowledgebase (CDEK) is a platform intended to explore every active pharmaceutical ingredient (API) with evidence of clinical testing | YOU AGREE THAT THE INFORMATION PROVIDED ON THIS WEBSITE IS PROVIDED “AS IS”, WITHOUT ANY WARRANTY OF ANY KIND, EXPRESSED OR IMPLIED, INCLUDING WITHOUT LIMITATION WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE, OR NON-INFRINGEMENT OF ANY THIRD-PARTY PATENT, COPYRIGHT, OR ANY OTHER THIRD-PARTY RIGHT | Build your own query by selecting various table columns and a filtration predicate; then press the to launch the query
feature list: operation_0224
feature list: operation 3431
software help: about

CDMetaPOP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0610
application sub category: topic_0621
application sub category: topic 3053
citation: https://doi.org/10.1111/1755-0998.13121
citation: pubmed:31769930
description: Modeling multilocus selection in an individual-based, spatially-explicit landscape genetics framework. An individual-based, eco-evolutionary model for spatially-explicit simulation of population viability in landscape demogenetics. Welcome to the CDMetaPOP v1.0 release! This release includes installation instructions, version notes, some examples, and technical documentation. Baseline Requirements. CDMetaPOP requires the Python2.7.x interpreter, NumPy package, and SciPy package. Remember that Python modules usually require particular Python interpreters, so be sure the version ID for any external Python module or package (e.g. NumPy or others) matches the version of your Python interpreter (normally v2.7.x). aTo avoid Python installation errors, we highly recommend installing Python from any number of the freely available bundlers, e.g., Canopy, ActiveState, Anaconda.
feature list: operation_0337
feature list: operation 2426
feature list: operation 3659

CDRgator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3308
citation: molcells.2018.0413
citation: pmcid:PMC6449719
citation: pubmed:30759968
description: Web-based database, CDRgator (Cancer Drug Resistance navigator) for comparative analysis of gene expression signatures of cancer drug resistance.
feature list: operation 2495
feature list: operation 3223
feature list: operation 3482
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.jsp

CDSeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 2269
application sub category: topic 3170
application sub category: topic 3300
citation: https://doi.org/10.1101/2021.01.30.428954
citation: JOURNAL.PCBI.1007510
citation: pmcid:PMC6907860
citation: pubmed:31790389
description: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data. CDSeq MATLAB code. CDSeq is a novel computational complete deconvolution method for dissecting tissue heterogeneity. CDSeq: A complete deconvolution method for dissecting tissue heterogeneity. Added data-dilution option to speed up the algorithm. We provided explaination in the manuscript which you can find on bioRxiv. Check out the demo.m in CDSeq_012 for details
feature list: operation 2495
feature list: operation 3629
feature list: operation 3802
license: GPL-3.0

CEBA geoportail
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0621
application sub category: topic 3050
application sub category: topic 3174
application sub category: topic 3810
citation: BDJ.7.E37518
citation: pmcid:PMC6751219
citation: pubmed:31592221
description: A portal for geographic reference data for the Amazon.
feature list: operation 2428

CEMARA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3305
application sub category: topic 3325
application sub category: topic 3376
citation: pubmed:20841733
description: Collection of continuous and complete records of patients with rare diseases, and their follow-up through a web-based Information System.
feature list: operation 2422
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

CEPICS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2640
application sub category: topic 3382
citation: FGENE.2019.00966
citation: pmcid:PMC6792302
citation: pubmed:31649733
description: A Comparison and Evaluation Platform for Integration Methods in Cancer Subtyping. There are two comparison strategies for the NMI and ARI depending on the availability of true labels of patients. If you upload an empirical pre-determination of subtypes for samples by experts or clinicians based on clinical phenotypes, images or experience, CEPICS will take it as gold standard to compare. If you don’t have any subtype information, CEPICS will calculate NMI and ARI between the results of every two methods for each k, and then calculated the average NMI and ARI for each method at each k
feature list: operation_0531
feature list: operation 3432
feature list: operation 3435
license: GPL-2.0

CERENKOV2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2885
application sub category: topic 3474
application sub category: topic 3517
citation: s12859-019-2637-4
citation: pmcid:PMC6364436
citation: pubmed:30727967
description: Software pipeline and associated machine-learning framework for identifying regulatory single nucleotide polymorphisms (rSNPs) in the noncoding genome for post-analysis of genetic regions identified in genome-wide association studies (GWAS).
feature list: operation_0484
feature list: operation 2495
feature list: operation 3661
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: v0.1-alpha
primary contact: Stephen Ramsey

Computational Environment for Radiological Research (CERR)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 3384
application sub category: topic 3444
citation: https://doi.org/10.1101/772178
citation: https://doi.org/10.1101/773929
description: Library of model implementations for sharing deep-learning image segmentation and outcomes models | Deep learning-based auto-segmentation of swallowing and chewing structures in CT | Matlab based platform for Radiological Research | CERR (pronounced 'sir'), stands for Computational Environment for Radiological Research. CERR is MATLAB based software platform for developing and sharing research results using radiation therapy treatment planning and imaging informatics. CERR has a wide variety of dose, imaging, and structure analysis and comparison tools. CERR is open-source and GNU GPL copyrighted
feature list: operation 3096
license: LGPL-2.1
software help: wiki

CEVIChE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0208
application sub category: topic_0625
application sub category: topic 3308
citation: GKZ805
citation: pmcid:PMC6821211
citation: pubmed:31552418
description: Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction | Transcriptional perturbation signatures are valuable data sources for functional genomics. Linking perturbation signatures to screenings opens the possibility to model cellular phenotypes from expression data and to identify efficacious drugs. We linked perturbation transcriptomics data from the LINCS-L1000 project with cell viability information upon genetic (Achilles project) and chemical (CTRP screen) perturbations yielding more than 90 000 signature-viability pairs. An integrated analysis showed that the cell viability signature is a major factor underlying perturbation signatures. The signature is linked to transcription factors regulating cell death, proliferation and division time
feature list: operation 3501
feature list: operation 3642
feature list: operation 3891

CEthreader
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0102
application sub category: topic_0130
application sub category: topic_0736
application sub category: topic 3474
citation: JOURNAL.PCBI.1007411
citation: pmcid:PMC6818797
citation: pubmed:31622328
description: Detecting distant-homology protein structures by aligning deep neural-network based contact maps. fold recorgnition by eigen-decomposition of contact map. CEthreader (Contact Eigenvector-based threader) is a new threading algorithm that combines contact-map with profile-based alignments for protein fold recognition.
feature list: operation_0272
feature list: operation_0300
feature list: operation_0303
feature list: operation_0476
feature list: operation_0477

CF-targeter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3407
citation: ACSSYNBIO.9B00070
citation: pubmed:31518497
description: A Rational Biological Cell Factory Targeting Platform for Biosynthetic Target Chemicals | Chassis selection from 70 candidate orgainisms for more than 6,000 target molecules production | CF-Targrter: We present CF-Targeter to solve several biological problems, including host organism selection, biosynthetic pathway design and quantitative evaluations of pathways. It is very useful for those who plan to biosynthesize a target molecule but do not know which host organism should be selected, what the heterologous pathway is or what maximum theoretical yields could be achieved | Tips: please choose a search type
feature list: operation 3799
feature list: operation 3803

Conserved Feature Discovery (CFD)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0203
application sub category: topic 2269
application sub category: topic 3170
application sub category: topic 3518
citation: https://doi.org/10.1101/833624
description: A statistical method for identifying consistently important features across samples. (software for the manuscript "A statistical method for identifying consistently important features across conditions"). CFD itself is implemented in Go (source code is in the go/src/ directory), and figures for the manuscript were generated in Python, using the produce_manuscript_figures.py code
feature list: operation 2495
feature list: operation 3435
feature list: operation 3630

Cell-Free Epigenome Atlas (CFEA)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 3173
application sub category: topic 3176
citation: GKZ715
citation: pmcid:PMC6943076
citation: pubmed:31428785
description: A cell-free epigenome atlas in human diseases | Search and download the information for the Mutual exclusivity. MutExGenome is a database of Mutual Exclusive mutations in mutiple species | Welcome to CFEA (Cell-Free Epigenome Atlas) | The cell-free DNA (cfDNA) was shown to be a powerful tool for the noninvasive diagnosis of various diseases and accumulating evidence suggests large-scale epigenetic alterations such as cfDNA methylation (5mC), cfDNA hydroxymethylation (5hmC) and cfDNA nucleosome positioning (NP) can sensitively detect and classify cancers. The CFEA (Cell-Free Epigenome Atlas) data portal is the first database dedicated to human cell-free epigenomes
feature list: operation_0432
feature list: operation 2428
feature list: operation 3192

CFNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3382
application sub category: topic 3474
citation: BTZ353
citation: pmcid:PMC6612823
citation: pubmed:31510662
description: Rotation equivariant and invariant neural networks for microscopy image analysis | Conic Convolution and DFT Network (CFNet) combines a novel rotation equivariant convolution scheme, called conic convolution, and the DFT to aid networks in learning rotation-invariant tasks. This network has been especially designed to improve performance of CNNs on automated computational tasks related to microscopy image analysis
feature list: operation 3443

CFQuant-automatic
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3301
application sub category: topic 3382
citation: mSphere.00676-18
citation: pmcid:PMC6315083
citation: pubmed:30602526
description: Analyzes images of cell colonies that emit a luminescent/fluorescent signal in the form of a luminescent halo around the colony. Automatically identifies both the colonies and their emitted luminescent halos and returns quantitative data on features
feature list: operation 3799
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Eyal Dafni

Clinical Genome and Ancestry Report (CGAR)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0208
application sub category: topic_0625
application sub category: topic 2640
application sub category: topic 3673
application sub category: topic 3676
author: In-Hee Lee
author: Jose A. Negron
citation: humu.23942
citation: pmcid:PMC7180092
citation: pubmed:31691385
contributor: https://orcid.org/0000-0002-8029-7160
description: An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. Clinical Genome & Ancestry Report (CGAR) enables users to identify and prioritize phenotype-associated variants from genome sequencing with a user-friendly and interactive online platform.
feature list: operation 3196
feature list: operation 3226
feature list: operation 3227
feature list: operation 3675
software help: latest
primary contact: Sek-Won Kong

CGIDLA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
citation: TCBB.2019.2935971
citation: pubmed:31443042
description: Developing the Web Server for CpG Island related Density and LAUPs (Lineage-associated Underrepresented Permutations) Study | WA web server for CpG Island study:CpG Island related density and LAUPs (Lineage-associated Underrepresented Permutations) analysis
feature list: operation_0430
feature list: operation_0440
feature list: operation 3431

CGIdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0208
application sub category: topic 2640
application sub category: topic 3360
citation: J.OMTN.2019.07.003
citation: pmcid:PMC6700431
citation: pubmed:31400611
description: Genetic Interaction-Based Biomarkers Identification for Drug Resistance and Sensitivity in Cancer Cells | Cancer cells generally harbor hundreds of alterations in the cancer genomes and act as crucial factors in the development and progression of cancer | However, detection of genetic interactions in the cancer genome is a major obstacle in the research of identifying biomarkers for cancer cell drug resistance and sensitivity
feature list: operation 3501

CGLFold
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0196
application sub category: topic 3542
citation: BTZ943
citation: pubmed:31860059
description: A contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm.
feature list: operation_0476
feature list: operation_0481
feature list: operation 3454

CGR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0102
application sub category: topic 3320
application sub category: topic 3474
application sub category: topic 3512
citation: J.YGENO.2019.10.018
citation: pubmed:31704313
description: Splice sites detection using chaos game representation and neural network. Email: hoangthanhtungvn@gmail.com. Project description: We propose to use chaos game representation and neural network for splice sites detection. DNA sequences are mapped to numerical sequences using chaos game representation. Numerical sequences are used as feature inputs to neural networks for splice sites classification
feature list: operation_0232
feature list: operation_0446
feature list: operation 2871

CGRtools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic 2258
application sub category: topic 3068
author: Ramil Nugmanov
citation: ACS.JCIM.9B00102
citation: pubmed:31063394
description: Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing | CGRs, molecules and reactions manipulation.
feature list: operation_0394
feature list: operation 3798
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: cgrtools.readthedocs.io
primary contact: Alexandre Varnek
primary contact: Ramil Nugmanov
primary contact: Timur Madzhidov

CHARMM-GUI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0152
application sub category: topic_0153
citation: jcc.20945
citation: jcc.23702
citation: acs.jctc.5b00935
citation: acs.jctc.8b01066
citation: pubmed:18351591
citation: pubmed:25130509
citation: pubmed:26631602
citation: pubmed:30525595
description: Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans.
feature list: operation_0417
feature list: operation 2476
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

CHERIPIC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0199
citation: s12859-018-2515-5
citation: pmcid:PMC6323790
citation: pubmed:30616525
description: Computing Homozygosity Enriched Regions In genomes to Prioritize Identification of Candidate variants (CHERIPIC) - tools to pick causative mutation from bulks segregant sequencing.
feature list: operation_0524
feature list: operation 3226
feature list: operation 3227
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: 2.-Usage-Instructions
software version: 1.2.6
primary contact: Shyam Rallapalli

CHOmine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: An integrated database for Cricetulus griseus and CHO cells
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 1.0.0

CHiCP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3173
citation: btw173
citation: pmcid:PMC4978926
citation: pubmed:27153610
description: Web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.
feature list: operation_0438
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: docs
primary contact: O. S. Burren

CIBERSORT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 2640
citation: nmeth.3337
citation: pmcid:PMC4739640
citation: pubmed:25822800
description: The Role of Circular RNA CDR1as/ciRS-7 in Regulating Tumor Microenvironment | CIBERSORT is an analytical tool developed by Newman et al. to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data | Absolute mode (beta) is now available
feature list: operation 2436
feature list: operation 3463
feature list: operation 3792

Causal Inference Enrichment (CIE)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0204
application sub category: topic_0625
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3170
citation: gkz1046
citation: pmcid:PMC7145661
citation: pubmed:31701125
description: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators. Causal Inference and Directional Enrichment Methods on Biological Networks. Launching Causal Inference Engine... CIE is a platform for inference of active transcriptional regulators of differential gene expression. CIE provides a user-friendly web-app and an R-package to run inference queries on casual regulatory netowrks. Several regulatory networks are provided in the platform, including a TF-gene intraction network constructed from ChIP-seq and tissue specific gene expression data, a netowrk based on STRING-DB, and curated TF-gene interaction networks such as TRRUST and TRED. The R-package provides functionality for custom networks as well. Causal Inference Engine: Directional Enrichment Analysis on Biological Networks.
feature list: operation 1781
feature list: operation 2436
feature list: operation 3083
feature list: operation 3439

CINNA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
citation: bty819
citation: pubmed:30239607
description: Central Informative Nodes in Network Analysis (CINNA) package gathers all required functions for centrality analysis in weighted/unweighted and directed/undirected networks.
feature list: operation 2497
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: CINNA.pdf
software help: CINNA.html
software version: 1.1.53
primary contact: Minoo Ashtiani

CIRCexplorer2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3068
application sub category: topic 3320
application sub category: topic 3512
author: Li Yang
author: Xiao-Ou Zhang
citation: 978-1-4939-8808-2 10
citation: pubmed:30539552
description: Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
software help: latest

CIRI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic 3320
application sub category: topic 3512
citation: s13073-019-0614-1
citation: pmcid:PMC6339429
citation: pubmed:30660194
description: CircRNA Identifier. A de novo circular RNA identification tool.
feature list: operation_0443
feature list: operation 3644
feature list: operation 3799
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: download
primary contact: Fangqing Zhao
primary contact: Jinyang Zhang

CISI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0593
application sub category: topic 3379
citation: S12539-019-00330-1
citation: pubmed:31119495
description: Tool for Predicting Cross-interaction or Self-interaction of Monoclonal Antibodies Using Sequences.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Jian Huang

CITE-seq-Count
type: SoftwareApplication
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1930
input: Sequence feature label
  type: FormalParameter
  additional type: data 1022
  encoding format: format 3752
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 3750
output: Nucleic acid report
  type: FormalParameter
  additional type: data 2084
  encoding format: format 3033
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2830
application sub category: topic 3308
description: Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.
feature list: operation 3800
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: CITE-seq-Count

CIViCmine
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0218
application sub category: topic_0219
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3474
citation: S13073-019-0686-Y
citation: s13073-019-0686-y
citation: pmcid:PMC6891984
citation: pubmed:31796060
description: CIViCmine is a literature-mined database of clinically relevant cancer biomarkers from data from PubMed and Pubmed Central Open Access subset.
feature list: operation_0306
feature list: operation 1812
feature list: operation 3778
license: MIT

CIViCpy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2640
application sub category: topic 3379
application sub category: topic 3400
citation: https://doi.org/10.1101/783134
citation: CCI.19.00127
description: A Python software development and analysis toolkit for the CIViC knowledgebase | Clinical Interpretations of Variants in Cancer | CIViCpy — civicpy 1.0.0-rc1 documentation | A python interface for the CIViC db application | Sorry, something went wrong. Reload? | Sorry, we cannot display this file | CIViCpy is an analysis toolkit and SDK for extracting and analyzing knowledge from the CIViC knowledgebase | You have reached the code repository for CIViCpy, a python client and analysis toolkit for the Clinical Interpretations of Variants in Cancer knowledgebase (CIViC) | Sorry, this file is invalid so it cannot be displayed | CIViCpy lets you pull data from CIViC using the civic module and interact with records as dynamic objects. With the aid of caching, it is easy to explore relationships between CIViC records (e.g. assertions, genes, variants) without worrying about querying CIViC more than once for the same data
feature list: operation 1812
feature list: operation 2422
feature list: operation 3197
license: MIT

CLASTR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic 2229
author: 0000-0001-6548-709X
description: CLASTR, the Cellosaurus STR similarity search tool enables users to compare one or more STR profiles with those available in the Cellosaurus cell line knowledge resource. It aims to help researchers in the process of cell line authentication and detecting potential contamination and misidentification cases.
feature list: operation 2233
is accessible for free: true
license: GPL-3.0
software help: help.html
software version: 1.2
primary contact: 0000-0001-6548-709X

CLIJ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic_0769
application sub category: topic 3372
application sub category: topic 3382
citation: S41592-019-0650-1
citation: pubmed:31740823
description: GPU-accelerated image processing for everyone. CLIJ is an OpenCL - ImageJ bridge and a Fiji plugin allowing users with entry-level skills in programming to build GPU-accelerated workflows to speed up their image processing. Increased efforts were put on documentation, code examples, interoperability, and extensibility. CLIJ is based on ClearCL, JOCL, Imglib2, ImageJ and SciJava
feature list: operation 2409
feature list: operation 3443
software help: CLIJ2-cheatsheet V3.pdf
software help: installationInFiji

CLINE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0081
application sub category: topic 3168
application sub category: topic 3382
citation: S12859-019-3149-Y
citation: pmcid:PMC6819642
citation: pubmed:31660851
description: CLINE (Comparison of bioLogIcal deNdrogram structurEs), is a web-tool specifically designed for the visual comparison of dendrograms, with an emphasis on the display of matching clusters that, even when not isomorphic, can be perceived as having the same biological meaning.
feature list: operation_0570
feature list: operation 2938
feature list: operation 3432
license: MIT
software help: cline supplementary.pdf
software help: doc

CLIP-Explorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3794
description: Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to the iCLIP workflows also FLASH, and uvCLAP.

CLIPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0625
application sub category: topic 2640
application sub category: topic 3063
application sub category: topic 3379
application sub category: topic 3794
citation: https://doi.org/10.1101/814996
citation: journal.pone.0238290
citation: pmcid:PMC7500653
citation: pubmed:32946464
description: An interactive retrieval system for clinical trial studies with context-dependent protocol elements. Clinical trial protocol includes all the steps that should be conducted in clinical trial and all clinical trial start with development of the protocol. The purpose of our study is to provide context-dependent protocol element selection system for the development of objective and successful clinical trial protocols. We have developed a database and search application for protocol structure retrieval
feature list: operation 2421
feature list: operation 2422
feature list: operation 3891

CLOBNET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3376
application sub category: topic 3474
citation: CCI.18.00132
citation: pubmed:31454273
description: Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses | PURPOSE:We have created a cloud-based machine learning system (CLOBNET) that is an open-source, lean infrastructure for electronic health record (EHR) data integration and is capable of extract, transform, and load (ETL) processing. CLOBNET enables comprehensive analysis and visualization of structured EHR data. We demonstrate the utility of CLOBNET by predicting primary therapy outcomes of patients with high-grade serous ovarian cancer (HGSOC) on the basis of EHR data. MATERIALS AND METHODS:CLOBNET is built using open-source software to make data preprocessing, analysis, and model training user friendly. The source code of CLOBNET is available in GitHub
license: BSD-2-Clause

CLiP Chlamydomonas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0153
application sub category: topic 3794
citation: s41588-019-0370-6
description: Chlamydomonas Library Project (CLiP) provides access to a collection of mutant strains in the green alga Chlamydomonas reinhardtii, a powerful model system for studying a broad range of fundamental processes including the biology of chloroplasts, photosynthesis, cilia/flagella, eyespots, and algal lipid accumulation.
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: Jonikas lab
primary contact: Matt Laudon

Clinical MetaData Ontology (CMDO)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Ontology
application sub category: topic_0089
application sub category: topic 3379
application sub category: topic 3400
citation: S12911-019-0877-X
citation: pmcid:PMC6701018
citation: pubmed:31429750
description: A simple classification scheme for data elements of clinical data based on semantics
feature list: operation 2422
feature list: operation 3352
feature list: operation 3559

CytoMegaloVirus DataBase (CMVdb)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0202
application sub category: topic_0804
application sub category: topic 3324
application sub category: topic 3421
application sub category: topic 3489
citation: S12539-019-00350-X
citation: pubmed:31813095
description: A Public Omics Database for Systematic and Comparable Information of CMV. Cytomegalovirus is a double-stranded DNA virus in the same family as herpesvirus found every where,infect people of all ages. Cytomegalovirus Treatment & Management Kauser Akhter, MD Assistant Professor, Department of Internal Medicine, Florida State University College of Medicine; Associate Program Director, Infectious Diseases Fellowship Program, Orlando Health; Updated: Jan 05, 2017
feature list: operation_0308
feature list: operation_0477
feature list: operation 2421

CNAPE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 2885
application sub category: topic 3170
application sub category: topic 3474
application sub category: topic 3518
citation: TCBB.2019.2944827
citation: pubmed:31581092
description: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression. [Source] CNAPE: A Software for Copy Number Alteration Prediction from Gene Expression in Human Cancers. Copy number alterations (CNAs) are important features of human cancer. While the standard methods for CNA detection (CGH arrays, SNP arrrays, DNA sequencing) rely on DNA, occasionally DNA data are not available, especially in cancer studies (e.g. biopsies, legacy data). CNAPE comes into play by predicting CNAs based on gene expression data from RNA-seq
feature list: operation 2454
feature list: operation 2495
feature list: operation 3435

CNAtra
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0749
application sub category: topic 2640
application sub category: topic 3673
citation: https://doi.org/10.1101/639294
description: Hierarchical Discovery of Large-scale and Focal Copy Number Alterations in Low-coverage Cancer Genomes.
feature list: operation 3196
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: CNAtra User Guide.pdf
primary contact: Ahmed Khalil

CNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3318
application sub category: topic 3382
application sub category: topic 3474
citation: S41598-019-53551-1
citation: pmcid:PMC6874599
citation: pubmed:31758002
description: Convolutional neural network for efficient estimation of regional brain strains. Three pretrained CNN neural network models are provided based on all of the brain response samples available in the published study (N=3069). They correspond to the peak maximum principal strain (MPS) of the whole brain (WB), MPS of the corpus callosum (CC), and fiber strain (FS) of the CC, all assessed at the 95th percentile levels
feature list: operation 2426
feature list: operation 3435
feature list: operation 3659
license: GPL-3.0

CNN-SuccSite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0160
application sub category: topic_0601
application sub category: topic 3474
application sub category: topic 3520
citation: S41598-019-52552-4
citation: pmcid:PMC6838336
citation: pubmed:31700141
description: Problems with homepage (January 6th, 2021) | CNN-SuccSite is a web server for characterization and identification succinylation sites based on deep learning method.
feature list: operation_0417
feature list: operation 3755

CNN-T4SE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic 3172
application sub category: topic 3474
application sub category: topic 3542
citation: BBZ120
citation: pubmed:31860715
description: Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery. CNN-based Annotation of Bacterial Type IV Secretion System Effectors. The CNN-T4SE is a tool that can be run in windows and linux operating systems. It is used to identify effector proteins through the amino acid sequence, evolutionary information in the form of a position-specific scoring matrix, secondary structure and solvent accessibility information of the proteins.
feature list: operation_0267
feature list: operation 2476
feature list: operation 2488
operating system: Linux
operating system: Windows
software help: User Manual of CNN-T4SE.pdf

CNV-BAC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0654
application sub category: topic 3673
citation: btaa208
citation: https://doi.org/10.1101/2019.12.24.887992
citation: pubmed:32219377
description: Copy Number Variation Detection in Bacterial Circular Genome. Abstract Motivation Whole genome sequencing (WGS) is widely used for copy number variation (CNV) detection. However, for most bacteria, their circular genome structure and high replication rate make reads more enriched near the replication origin. CNV detection based on read depth could be seriously influenced by such replication bias. Results We show that the replication bias is widespread using ~200 bacterial WGS data. We develop CNV-BAC that can properly normalize the replication bias as well as other known biases in bacterial WGS data and can accurately detect CNVs. Simulation and real data analysis show that CNV-BAC achieves the best performance in CNV detection compared with available algorithms. Availability and implementation CNV-BAC is available at https: github.com LinjieWu CNV-BAC. Contact ruibinxi@math.pku.edu.cn
feature list: operation 3196
feature list: operation 3435

CNVRanger
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3518
citation: btz632
citation: pmcid:PMC9887538
citation: pubmed:31392308
description: association analysis of CNVs with gene expression and quantitative phenotypes | Summarization and expression/phenotype association of CNV ranges | The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes
feature list: operation_0484
feature list: operation 3232
feature list: operation 3800
license: Artistic-2.0

CNVScope
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3170
citation: https://doi.org/10.1177/1176935119890290
citation: pmcid:PMC6887803
citation: pubmed:31832011
description: Visually Exploring Copy Number Aberrations in Cancer Genomes. CNVScope interchromosomal heatmaps. A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization. Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps. CNVScope is a visualization toolkit for seeing copy number data in a relationship fashion, both utilizing tools that find regions of interest (much like domains in Hi-C terminology), visualize the relationships in vibrant color (blue for negative association, red for positive), and integrates several different relevant types of data (RNASeq, sample information, Cancer Gene Census data, and structural variants)
feature list: operation_0337
feature list: operation 2429
feature list: operation 3196
feature list: operation 3659
license: BSD-3-Clause

CNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic_0625
citation: btz441
citation: pmcid:PMC6954662
citation: pubmed:31141125
description: Multi-omics Approach to Detecting Clinically Associated, Combinatory Genomic Signatures.
feature list: operation 2495
feature list: operation 3192
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Zhongming Zhao

COAC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0208
application sub category: topic_0602
application sub category: topic 3360
citation: journal.pcbi.1006772
citation: pmcid:PMC6396937
citation: pubmed:30779739
description: Component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications.
feature list: operation 1781
feature list: operation 3463
feature list: operation 3766
is accessible for free: true
license: MPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: ChengF-Lab

COBRA Toolbox
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 2258
application sub category: topic 3172
citation: s41596-018-0098-2
citation: pmcid:PMC6635304
citation: pubmed:30787451
description: Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: cobratoolbox
software help: index.html
software version: 3.0
primary contact: Ronan Fleming on behalf of the COBRA Toolbox Development Community

CODA-ML
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 3300
application sub category: topic 3407
citation: s12859-019-2812-7
citation: pmcid:PMC6538558
citation: pubmed:31138123
description: Context-specific biological knowledge representation for systemic physiology analysis.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

COLMARm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0593
application sub category: topic 3172
application sub category: topic 3444
citation: 978-1-4939-9690-2 24
citation: ACS.JPROTEOME.9B00845
citation: pubmed:31463859
citation: pubmed:32073269
description: Automated Tools for the Analysis of 1D-NMR and 2D-NMR Spectra | COLMARm 13C-1H HSQC, HSQC-TOCSY and TOCSY Query and Verification | Visit a step by step how-to with figures here | Bingol, K.; Li, DW.; Zhang, B.; Brüschweiler, R.; Comprehensive metabolite identification strategy using multiple two-dimensional NMR spectra of a complex mixture implemented in the COLMARm web server; Anal. Chem; 2016, 88, 12411-12418;
feature list: operation 3215
feature list: operation 3629
feature list: operation 3803

COMBIgor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0089
application sub category: topic 3382
application sub category: topic 3855
citation: ACSCOMBSCI.9B00077
citation: pubmed:31121098
description: Data-Analysis Package for Combinatorial Materials Science.
feature list: operation 1812
feature list: operation 3431
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: install
software help: tutorial

COMMAND
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3518
citation: s12859-019-2643-6
citation: pmcid:PMC6348648
citation: pubmed:30691411
description: Web-based application used to download, collect and manage gene expression data from public databases.
feature list: operation 2495
feature list: operation 3431
feature list: operation 3800
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Marco Moretto

COMUNET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
citation: btaa482
citation: https://doi.org/10.1101/864686
citation: pmcid:PMC7520036
citation: pubmed:32399572
description: A tool to explore and visualize intercellular communication. Abstract Intercellular communication plays an essential role in multicellular organisms and several algorithms to analyse it from single-cell transcriptional data have been recently published, but the results are often hard to visualize and interpret. We developed COMUNET (Cell cOMmunication exploration with MUltiplex NETworks), a tool that streamlines the interpretation of the results from cell-cell communication analyses. COMUNET uses multiplex networks to represent and cluster all potential communication pathways between cell types. The algorithm also enables the search for specific patterns of communication and can perform comparative analysis between two biological conditions. To exemplify its use, here we apply COMUNET to investigate cell communication patterns in single-cell transcriptomic datasets from mouse embryos and from an acute myeloid leukemia patient at diagnosis and after treatment
feature list: operation_0337
feature list: operation 3432
feature list: operation 3802

CONFINED
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic 3295
application sub category: topic 3518
citation: s13059-019-1743-y
citation: pmcid:PMC6624895
citation: pubmed:31300005
description: CCA (canonical correlation analysis) ON Features for INter-dataset Effect Detection.
feature list: operation 3196
feature list: operation 3501
feature list: operation 3798
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Mike Thompson

COPO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0780
application sub category: topic 3174
application sub category: topic 3810
citation: https://doi.org/10.1101/782771
description: COPO is a portal for plant scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results.
feature list: operation 3431
feature list: operation 3435
feature list: operation 3436
is accessible for free: true

CORDERLY
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0196
application sub category: topic_0602
application sub category: topic 3382
citation: ACS.LANGMUIR.9B02877
citation: pubmed:31702166
description: The CORDERLY software analyses colloidal ordering via the 2D fast Fourier transform, the radial distribution function, the spatial distribution function, and the angular distribution. The spatial distribution function plots the resulting analysis in Cartesian and polar coordinates (angular distribution).
feature list: operation_0310
feature list: operation_0337
feature list: operation 3443
license: GPL-3.0

CORE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0654
application sub category: topic 2640
citation: 978-1-4939-8868-6 4
citation: pubmed:30378070
description: Cores of Recurrent Events (CORE) is software tool for delineating regions of recurrent DNA copy number alteration in cancer.
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: CORE.pdf
software version: 3.0
primary contact: Guoli Sun

CORGi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3175
application sub category: topic 3407
citation: s12859-018-2539-x
citation: pmcid:PMC6302372
citation: pubmed:30577744
description: CORGi (COmplex Rearrangement detection with Graph-search), a method for the detection and visualization of complex local genomic rearrangements.
feature list: operation_0452
feature list: operation 3185
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
primary contact: J. P. Kocher

COSS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: https://doi.org/10.1101/640458
description: COSS (CompOmics Spectral Searching ) is a user-friendly spectral library search tool capable of processing large spectral libraries and supporting multiple file formats.
feature list: operation 3637
feature list: operation 3649
feature list: operation 3801
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software version: 1.0.0
primary contact: Computational Omics and Systems Biology Group

Codon Usage Similarity Index (COUSIN)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0091
application sub category: topic_0154
application sub category: topic_0203
application sub category: topic_0780
application sub category: topic 3512
citation: EVZ262
citation: pmcid:PMC6934141
citation: pubmed:31800035
description: A Normalized Measure of Codon Usage Preferences. COUSIN is a bioinformatic tool which aims to calculate the Codon Usage Preferences (CUPrefs) of sequences using a novel index named COUSIN. In addition, numerous functions are proposed to enhance your CUPrefs analysis experience !
feature list: operation_0284
feature list: operation_0285
feature list: operation_0335
feature list: operation 2962
feature list: operation 3435

COXMEG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3517
citation: https://doi.org/10.1101/729285
citation: genetics.119.302940
citation: pmcid:PMC7198273
citation: pubmed:32132097
description: Genome-wide association analysis of age-at-onset traits using Cox mixed-effects models | Abstract Age-at-onset is one of the critical phenotypes in cohort studies of age-related diseases. Large-scale genome-wide association studies (GWAS) of age-at-onset can provide more insights into genetic effects on disease progression, and transitions between different stages. Moreover, proportional hazards or Cox regression generally achieves higher statistical power in a cohort study than a binary trait using logistic regression. Although mixed-effects models are widely used in GWAS to correct for population stratification and family structure, application of Cox mixed-effects models (CMEMs) to large-scale GWAS are so far hindered by intractable computational intensity. In this work, we propose COXMEG, an efficient R package for conducting GWAS of age-at-onset using CMEMs
feature list: operation 3196
feature list: operation 3659
feature list: operation 3891

CPGAVAS2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic 2885
application sub category: topic 3170
application sub category: topic 3512
citation: GKZ345
citation: pmcid:PMC6602467
citation: pubmed:31066451
description: Integrated plastome sequence annotator and analyzer.
feature list: operation_0464
feature list: operation_0484
feature list: operation_0526
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial cpgavas.pdf
primary contact: Chang Liu

CPMCGLM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2269
application sub category: topic 3305
citation: s12874-019-0711-2
citation: pmcid:PMC6469151
citation: pubmed:30991962
description: R package for p-value adjustment when looking for an optimal transformation of a single explanatory variable in generalized linear models.
feature list: operation 3659
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: CPMCGLM
software version: 1.2

CPPE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0593
application sub category: topic 3343
application sub category: topic 3892
citation: ACS.JCTC.9B00758
citation: pubmed:31580670
description: An Open-Source C++ and Python Library for Polarizable Embedding. C++ and Python library for Polarizable Embedding. CPPE is an open-source, light-weight C-Plus-Plus library for Polarizable Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE for ground-state self-consistent field calculations and post-SCF methods. A convenient Python interface is also available
license: LGPL-3.0

Cancer Predisposition Sequencing Reporter (CPSR)
type: SoftwareApplication
input: Sequence variations
  type: FormalParameter
  additional type: data 3498
  encoding format: format 3016
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2331
  encoding format: format 3464
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0622
application sub category: topic_0769
application sub category: topic 2640
application sub category: topic 3168
application sub category: topic 3360
application sub category: topic 3577
author: https://orcid.org/0000-0001-8468-2050
author: https://orcid.org/0000-0002-7502-7545
citation: ijc.33749
citation: pubmed:34310709
contributor: https://orcid.org/0000-0002-7502-7545
description: The Cancer Predisposition Sequencing Reporter (CPSR) is a computational workflow that interprets and classifies germline DNA variants identified from next-generation sequencing in the context of cancer predisposition and inherited cancer syndromes. The workflow can also report incidental findings (ACMG v3.0) as well as the genotypes of common germline variants associated with cancer risk, as reported in the NHGRI-EBI GWAS catalog.
feature list: operation_0331
feature list: operation 3225
feature list: operation 3226
feature list: operation 3661
feature list: operation 3672
is accessible for free: true
license: MIT
software help: cpsr
software help: installation.html
software help: all-options
software help: citation
software help: getting-started
software version: 1.0.0
primary contact: https://orcid.org/0000-0001-8468-2050

CPlantBox
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 3300
application sub category: topic 3810
application sub category: topic 3855
citation: diaa001
citation: https://doi.org/10.1101/810507
description: whole plant modelling framework for the simulation of water and carbon related processes. Output of CPlantBox-PiafMunch coupling. Simulation output of CPlantBox-PiafMunch coupling. Example 2-4
feature list: operation 2426
feature list: operation 3454
feature list: operation 3799
license: GPL-3.0

CQF-deNoise
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3173
citation: https://doi.org/10.1101/723833
description: K-mer counting with low memory consumption enables fast clustering of single-cell sequencing data without read alignment | CQF-deNoise enables fast k-mer counting with memory usage nearly unaffected by sequencing errors
feature list: operation_0524
feature list: operation 3198
feature list: operation 3472

CRAFT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Ontology
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic_0219
citation: BAX087
citation: pubmed:31725864
description: The Colorado Richly Annotated Full Text Corpus (CRAFT) is a manually annotated corpus consisting of 67 full-text biomedical journal articles from the PubMed Central Open Access Subset.
feature list: operation 2421
feature list: operation 3280
feature list: operation 3778
is accessible for free: true
license: CC-BY-3.0

CRA toolbox
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 2640
citation: s12859-019-2933-z
citation: pmcid:PMC6617887
citation: pubmed:31288758
description: Software package for conditional robustness analysis of cancer systems biology models in MATLAB.
feature list: operation 2426
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: home

CRB-Anim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 3500
description: CRB-Anim is the online catalog of biological resources of the french national infrastructure supporting research on domestic animals.

CRC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 2259
application sub category: topic 2269
application sub category: topic 2640
citation: https://doi.org/10.1101/633180
description: Conditional Robust Calibration (CRC) - Bayesian method for nonlinear model calibration and robustness analysis using omics data.
feature list: operation 3799
is accessible for free: true
license: Unlicense
operating system: Linux
software help: README.md
primary contact: Fortunato Bianconi

CRCRpred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3360
citation: https://doi.org/10.1101/639740
description: Colo-Rectal Cancer Risk Prediction (CRCRpred) webserver can be used to distinguish high risk CRC patients from low risk CRC patients given the protein concentration of one or more apoptotic proteins (Bak, Bax, Bcl2, BclXL or Mcl1) involved in the process of Mitochondrial Outer Membrane Permeabilization (MOMP), which is defunct in the case of cancer. The risk estimation is based on statistical and survival analysis on recent CRC datasets.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
primary contact: Gajendra P. S. Raghava

Consensus Reverse Docking System (CRDS)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 3336
citation: BTZ656
citation: pubmed:31432077
description: Consensus Reverse Docking System for Target Fishing | Identification of putative drug targets is a critical step for explaining the mechanism of drug action against multiple targets, finding new therapeutic indications for existing drugs, and unveiling the adverse drug reactions. One important approach is to use the molecular docking. However, its widespread utilization has been hindered by the lack of easy-to-use public servers. Therefore, it is vital to develop a streamlined computational tool for target prediction by molecular docking on a large scale. RESULTS:We present a fully automated web tool named CRDS (Consensus Reverse Docking System) which predicts potential interaction sites for a given drug. To improve hit rates, we developed a strategy of consensus scoring
feature list: operation_0478

CREAM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3169
citation: GR.248658.119
citation: pmcid:PMC6771399
citation: pubmed:31533978
description: Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks | Clustering of Genomic Regions Analysis Method | Provides a new method for identification of clusters of genomic regions within chromosomes. Primarily, it is used for calling clusters of cis-regulatory elements (COREs). 'CREAM' uses genome-wide maps of genomic regions in the tissue or cell type of interest, such as those generated from chromatin-based assays including DNaseI, ATAC or ChIP-Seq. 'CREAM' considers proximity of the elements within chromosomes of a given sample to identify COREs in the following steps: 1) It identifies window size or the maximum allowed distance between the elements within each CORE, 2) It identifies number of elements which should be clustered as a CORE, 3) It calls COREs, 4) It filters the COREs with lowest order which does not pass the threshold considered in the approach
feature list: operation_0441
feature list: operation 3432
feature list: operation 3501
license: GPL-3.0

CRH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Suite
application sub category: topic_0160
application sub category: topic_0736
citation: bty863
citation: pmcid:PMC6513158
citation: pubmed:30295745
description: cath-resolve-hits (CRH)- tool that resolves domain matches suspiciously quickly.
feature list: operation_0303
feature list: operation 3192
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: latest
primary contact: Ian Sillitoe
primary contact: Tony E Lewis

CRISPR-ERA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0204
application sub category: topic_0621
application sub category: topic_0749
citation: btv423
description: Design tool for CRISPR-mediated gene editing, repression and activation.
feature list: operation 3096
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.jsp
primary contact: Honglei Liu

CRISPR-P
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0659
application sub category: topic_0780
application sub category: topic 3810
citation: j.molp.2017.01.00
description: Improved CRISPR/Cas9 tool for genome editing in plants
feature list: operation 3096
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
software version: 2.0
primary contact: Kabin Xie
primary contact: Ling-Ling Chen

CRISPRCas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0080
description: Suite of web applications for analysing Clustered Regularly Interspaced Short Palindromic Repeats.

CRISPRCasFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic_0160
application sub category: topic_0798
citation: gky425
citation: pmcid:PMC6030898
citation: pubmed:29790974
description: Easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program with improved specificity and indication on the CRISPR orientation. MacSyFinder is used to identify cas genes, the CRISPR-Cas type and subtype.
feature list: operation 3211
operating system: Linux
operating system: Mac
software help: Help
software version: 1.0.5 - I2BC
primary contact: Christine Pourcel
primary contact: David Couvin
primary contact: Marie Touchon

CRISPR Explorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3173
application sub category: topic 3512
application sub category: topic 3912
author: Kenian Chen
citation: JBM.2016.138
citation: pmcid:PMC6706119
citation: pubmed:31453219
description: A fast and intuitive tool for designing guide RNA for genome editing | The RNA-guided CRISPR-Cas9 (clustered, regularly interspaced, short palindromic repeat-CRISPR-associated 9) system has become a revolutionary technology for targeted genome engineering. The critical step of this technology requires the design of a highly specific and efficient guide RNA (gRNA) that will guide the Cas9 nuclease to the complementary DNA target sequence. CRISPR-Explorer is a new and user-friendly web server for selecting optimal CRISPR sites. It implements the latest scoring schemes of gRNA specificity and efficiency based on published empirical studies. The gRNA design results are generated instantly, thus removing wait times. The user can visualize the high-quality gRNAs with detailed design information through an interactive genome browser. Furthermore, the user can define and specify the parameters for gRNA selection in the Batch Design mode, which recognizes various input formats
feature list: operation 3096

CRISPRdirect
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3512
citation: btu743
citation: pmcid:PMC4382898
citation: pubmed:25414360
description: Software for designing CRISPR/Cas guide RNA with reduced off-target sites.
feature list: operation 3211
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Yuki Naito

CRISPRitz
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 2885
application sub category: topic 3512
application sub category: topic 3676
application sub category: topic 3912
citation: BTZ867
citation: pubmed:31764961
description: A rapid, high-throughput, and variant-aware in silico off-target site identification for CRISPR genome editing. Tool package to perform in-silico CRISPR analysis and assessment. CRISPRitz is a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments.
feature list: operation 3096
feature list: operation 3211
feature list: operation 3454
license: GPL-3.0

CRISPRs Database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0157
application sub category: topic_0749
application sub category: topic 2885
citation: https://doi.org/10.1186/1471-2105-8-172
citation: pmcid:PMC1892036
citation: pubmed:17521438
description: Gateway to publicly accessible CRISPRs database.
primary contact: Christine Pourcel

CRM-SIRT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3383
application sub category: topic 3452
citation: BTZ787
citation: pubmed:31617571
description: A novel constrained reconstruction model towards high-resolution sub-tomogram averaging.

CROSSalive
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0082
application sub category: topic_0659
application sub category: topic 3512
citation: https://doi.org/10.1101/626085
description: Web server for predicting the in vivo structure of RNA molecules.
feature list: operation_0278
feature list: operation_0502
feature list: operation 2495
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation.html
software help: tutorial crossalive.html
primary contact: Gian Tartaglia

CRUMBLER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3810
citation: JOURNAL.PONE.0221471
citation: pmcid:PMC6709893
citation: pubmed:31449539
description: A tool for the prediction of ancestry in cattle | Added an avenue for data that plink does not have a "species ID" for. In this case users, will specify "NA" as the plink_species_ID in their input file. It is now required to specify chromosome number for the data in the input | CRUMBLER has now been successfully ran in Pigs, following these updates
feature list: operation_0335
feature list: operation 3196

CRUP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0204
application sub category: topic_0634
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3295
citation: S13059-019-1860-7
citation: pmcid:PMC6839171
citation: pubmed:31699133
description: A comprehensive framework to predict condition-specific regulatory units. We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data. Enhancers are subsequently assigned to different conditions and correlated with gene expression to derive regulatory units. We thoroughly test and then apply CRUP to a rheumatoid arthritis model, identifying enhancer-gene pairs comprising known disease genes as well as new candidate genes.
feature list: operation_0438
feature list: operation 3439
feature list: operation 3463

CRYSPLOT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3068
application sub category: topic 3314
citation: JCC.25858
citation: pubmed:31077416
description: Visualization environment for plotting properties of crystalline solids as computed by means of the CRYSTAL code.
feature list: operation_0337
feature list: operation 1812
feature list: operation 3454
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: what is.html
software help: 2017-09-19 11-09-42 CRYSTAL17 - User Manual.pdf

CS2BP2-Plot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0659
citation: S12859-019-2902-6
citation: pmcid:PMC6542128
citation: pubmed:31142266
description: Pairwise visual comparison of small RNA secondary structures with base pair probabilities.
feature list: operation_0278
feature list: operation_0502
feature list: operation_0570
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: about.html
primary contact: 0000-0003-1100-646X

CS2Structure
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0154
application sub category: topic_0593
citation: ACS.JPCB.9B09814
citation: pubmed:31829591
description: C2Structure: Extracting Structural Information Directly From NMR Chemical Shifts. Conditional Prediction of Ribonucleic Acid Secondary Structure Using Chemical Shifts.
feature list: operation_0267
feature list: operation_0278
feature list: operation_0303
feature list: operation 2441
license: MIT

CSESA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0632
application sub category: topic_0804
application sub category: topic 3673
citation: s12859-019-2806-5
citation: pmcid:PMC6486994
citation: pubmed:31029079
description: R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR.
feature list: operation_0308
feature list: operation 3840
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.2.0

CSF-PR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 3334
application sub category: topic 3360
application sub category: topic 3520
citation: 978-1-4939-9706-0 25
citation: pubmed:31432427
description: Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR) | Every year, a large number of published studies present biomarkers for various neurological disorders. Many of these studies are based on mass spectrometry proteomics data and describe comparison of the abundance of proteins in cerebrospinal fluid between two or more disease groups. As the number of such studies is growing, it is no longer straightforward to obtain an overview of which specific proteins are increased or decreased between the numerous relevant diseases and their many subcategories, or to see the larger picture or trends between related diseases
feature list: operation_0306
feature list: operation 3799

CSHMM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0160
application sub category: topic 2229
application sub category: topic 3170
citation: btz296
citation: pmcid:PMC6853676
citation: pubmed:31038684
description: Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data.
feature list: operation 3501
feature list: operation 3565
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README
primary contact: Ziv Bar-Joseph

CSI NGS Portal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Workflow
application sub category: topic_0769
application sub category: topic 3063
application sub category: topic 3168
application sub category: topic 3263
application sub category: topic 3794
citation: PREPRINTS201910.0146.V1
description: An Online Platform for Automated NGS Data Analysis and Sharing. CSI NGS Portal is an online platform for fully automated NGS data analysis and sharing . CSI NGS Portal uses a single, randomly generated, persistent, secure and http-only browser cookie for the sole purpose of user recognition for data authorisation.
feature list: operation 3096
feature list: operation 3222
feature list: operation 3799

Computation Subtraction-based Microbiome Discovery (CSMD)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0196
application sub category: topic_0637
application sub category: topic_0769
application sub category: topic 3174
application sub category: topic 3697
citation: BTZ790
citation: pubmed:31626280
description: A computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples. A computational pipeline for high-resolution profiling of low abundance microbiome in clinical samples using whole genome shotgun sequencing. Computation Subtraction-based Microbiome Discovery (CSMD). CSMD will work with a series of libraries listed in Table 2, including human-related genomes or sequences (21G) and all RefSeq bacteria genomes (150G, as of November 2018). The build process will then require approximately 500GB of additional disk space and 200GB of RAM. These genomes or sequences can be found in DBPATH/hg38/SEQ, DBPATH/AHG/SEQ, DBPATH/EHG/SEQ and DBPATH/RefSeq/bacteria/SEQ, respectively. And the indexed files will be saved in DBPATH/hg38, DBPATH/AHG, DBPATH/EHG and DBPATH/RefSeq/bacteria, respectively
feature list: operation 3198
feature list: operation 3454
feature list: operation 3460

Cell Topography Regression Learner (CTRL)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2229
application sub category: topic 3318
application sub category: topic 3382
application sub category: topic 3474
citation: https://doi.org/10.1101/817189
citation: jcs.245050
citation: pmcid:PMC7174840
citation: pubmed:32094267
description: A label-free method for dynamic measurement of single-cell volume. Kai Yao, Nash D Rochman, Sean X Sun (*ssun@jhu.edu) @ Johns Hopkins University
feature list: operation 3659
feature list: operation 3799
feature list: operation 3891
license: MIT

CVRMS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 3360
application sub category: topic 3517
citation: https://doi.org/10.1101/756130
description: Cross-validated Rank-based Marker Selection for Genome-wide Prediction of Low Heritability | Marker selection for genome-wide prediction | Cross-Validated Rank-based Marker Selection (CVRMS) | CVRMS is an R package designed to extract marker subset from ranked marker dataset induced by genome-wide association study (GWAS) or marker effect analysis for genome-wide prediction
feature list: operation 3196
feature list: operation 3557
feature list: operation 3659

Biobb Mutations Workflow
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic_0199
application sub category: topic_0769
author: Felix Xavier Amaladoss
description: CWL VM environment is a repository which can be deployed on cloud to execute Biobb Mutations Workflow.
is accessible for free: true
operating system: Linux
software version: 1.0

CYBERTRACK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2229
application sub category: topic 2269
application sub category: topic 3395
citation: S12859-019-3294-3
citation: pmcid:PMC6933651
citation: pubmed:31881827
description: Model-based cell clustering and population tracking for time-series flow cytometry data. CYBERTRACK is an R package for CYtometry-Based Estimation and Reasoning for cell populatiomn TRACKing
feature list: operation 2238
feature list: operation 3432
feature list: operation 3565

CYSMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0091
application sub category: topic_0634
application sub category: topic 3320
application sub category: topic 3382
application sub category: topic 3676
citation: HUMU.23941
citation: pubmed:31674704
description: An example of integrative tool for in silico analysis of missense variants identified in Mendelian disorders. Cystic Fibrosis Missense Analysis. Website dedicated to the in silico analysis of missense variants in the CFTR gene. Welcome to the Cystic Fibrosis Missense Analysis Website. Data provided and calculated by CYSMA must be considered as predictions. If you are dealing with the genetics of cystic fibrosis or CFTR-related disorders, you may find this website useful. CYSMA has been developed as a tool to help you to predict the impact of novel uncharacterized missense variants when the information provided by CFTR patient databases such as CFTR-France, CFTR1 and CFTR2 remain insufficient
feature list: operation_0331
feature list: operation 3197
feature list: operation 3461

CaFE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0176
application sub category: topic_0209
application sub category: topic_0804
citation: btw215
citation: pubmed:27153651
description: CaFE (Calculation of Free Energy) - a VMD plugin for binding affinity prediction using end-point free energy methods.
feature list: operation_0478
feature list: operation 2476
feature list: operation 3454
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: manual.pdf
primary contact: Tingjun Hou

CaPTk
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 3298
application sub category: topic 3384
application sub category: topic 3421
application sub category: topic 3444
citation: cci.19.00121
citation: pmcid:PMC6216519
citation: pmcid:PMC7113126
citation: pubmed:32191542
description: NIMG-70. QUANTITATIVE IMAGE ANALYSIS AND MACHINE LEARNING TECHNIQUES FOR DISTINGUISHING TRUE PROGRESSION FROM PSEUDOPROGRESSION IN PATIENTS WITH GLIOBLASTOMA. Perelman School of Medicine at the University of Pennsylvania. The Center for Biomedical Image Computing and Analytics (CBICA) was established in 2013, and focuses on the development and application of advanced computational and analytical techniques that quantify morphology and function from biomedical images, as well as on relating imaging phenotypes to genetic and molecular characterizations, and finally on integrating this information into diagnostic and predictive tools in an era of personalized medicine. Center for Biomedical Image Computing & Analytics. Cancer Imaging Phenomics Toolkit (CaPTk). CaPTk is a software platform for analysis of radiographic cancer images, currently focusing on brain, breast, and lung cancer
feature list: operation 3443
feature list: operation 3659
feature list: operation 3799

CaSiAn
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 3068
citation: bty281
citation: pmcid:PMC6129310
citation: pubmed:29668830
description: Calcium Signaling Analyzer (CaSiAn), an open source software tool that allows for quantifying these signal characteristics including individual spike properties and time course statistics in a semi-automated manner.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: started.html
primary contact: Alexander Skupin

Cafe Variome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic 3325
application sub category: topic 3489
citation: humu.22841
citation: pubmed:26224250
description: General‐purpose software for making genotype–phenotype data discoverable in restricted or open access contexts.
feature list: operation_0224
feature list: operation 3196
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: cafe variome user manual v2.docx

CancerA1DE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3474
citation: J.ISCI.2019.04.035
citation: pmcid:PMC6548890
citation: pubmed:31103852
description: Early Cancer Detection from Multianalyte Blood Test Results using Artificial Intelligence
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
software help: faq
primary contact: Ka-Chun Wong

CancerGeneNet
type: SoftwareApplication
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 3242
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
author: Elisa Micarelli
author: Prisca Lo SUrdo
citation: gkz871
citation: pmcid:PMC6943052
citation: pubmed:31598703
contributor: Marta Iannuccelli
description: CancerGeneNet is a resource that aims at linking genes that are frequently mutated in cancers to cancer phenotypes. The resource takes advantage of a curation effort aimed at embedding a large fraction of the gene products that are found altered in cancers in the cell network of causal protein relationships. Graph algorithms, in turn, allow to infer likely paths of causal interactions linking cancer associated genes to cancer phenotypes thus offering a rational framework for the design of strategies to revert disease phenotypes. CancerGenNet bridges two interaction layers by connecting proteins whose activities are affected by cancer gene products to proteins that impact on cancer phenotypes. This is achieved by implementing graph algorithms that allow searching for graph path that link any gene of interest to the “hallmarks of cancer".
feature list: operation 2497
is accessible for free: true
provider: Gianni Cesareni
primary contact: Luana Licata

CancerLSP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0654
application sub category: topic 3173
application sub category: topic 3375
citation: journal.pone.0221476
citation: pmcid:PMC6730898
citation: pubmed:31490960
description: Classification of early and late stage liver hepatocellular carcinoma patients from their genomics and epigenomics profiles | Liver Heptacellular Carcinoma Stage Prediction | CancerLSP is a web-bench Liver cancer stage prediction Server | Reference: Kaur H et. al., (2019) Classification of early and late stage liver hepatocellular carcinoma patients from their genomics and epigenomics profiles. https://doi.org/10.1371/journal.pone.0221476
feature list: operation_0417
feature list: operation 3206
feature list: operation 3207

CancerMine
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0218
application sub category: topic 2640
application sub category: topic 3474
citation: s41592-019-0422-y
citation: pubmed:31110280
description: Literature-mined resource for drivers, oncogenes and tumor suppressors in cancer.
feature list: operation_0306
feature list: operation 3431
feature list: operation 3501
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: cancermine
primary contact: Jake Lever

CancerSPP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3512
citation: s41598-019-52134-4
citation: pmcid:PMC6823463
citation: pubmed:31673075
description: Prediction and Analysis of Skin Cancer Progression using Genomics Profiles of Patients. A Webserver to Predict the Progression of Skin Cancer. This database maintains comprehensive information of short self-assembling peptides forming nanostructures and their structures. Reference: Bhalla, S., Kaur, H., Dhall, A., Raghava, GPS. Prediction and Analysis of Skin Cancer Progression using Genomics Profiles of Patients. Sci Rep 9, 15790 (2019) doi:10.1038/s41598-019-52134-4. https://doi.org/10.1038/s41598-019-52134-4. CancerSPP: A Webserver for predicting the progression of skin cancer. CancerSPP is a web-bench for skin cutaneous melanoma (SKCM) progression prediction
feature list: operation_0417
feature list: operation_0463
feature list: operation 3792
feature list: operation 3800

CancerTracer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0219
application sub category: topic 2640
application sub category: topic 3293
application sub category: topic 3360
citation: GKZ1061
citation: pubmed:31701131
description: a curated database for intrapatient tumor heterogeneity. CancerTracer is a manually curated and integrated database aims to help researchers to decipher tumor heterogeneity at individual patient level. It contains two types of tumor heterogeneity data: 1) Intra-tumor or Intra-metastatic heterogeneity: the presence of multiple subclones within a primary tumor or a single metastatic lesion; 2) Inter-metastatic heterogeneity: the presence of different subclones in different metastatic lesions of the same patient. Somatic mutations and copy number alterations are available in CancerTracer, since both of them are principal factors drive heterogeneity in cancer. The structured heterogeneity data enables researchers to identify trunk mutations in different cancer types and investigate the molecular mechanisms underlying intratumor heterogeneity
feature list: operation_0323
feature list: operation_0531
feature list: operation 2436

CandiMeth
type: SoftwareApplication
input: Experimental measurement
  type: FormalParameter
  additional type: data 3108
  encoding format: format 2330
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic 3307
description: Using existing tools in the Galaxy environment we generated the workflow CandiMeth (CANDIdate feature METHylation). This takes as input a differential methylation table from an R-based package and maps it to a reference genome build. A simple interface then allows the user to query the dataset with inputs as straightforward as lists of gene names, or as detailed as bed files containing specific chromosomal coordinates, for more sophisticated analyses.
feature list: operation 2409
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: candimeth-github
primary contact: Colum Walsh

Canvass
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic_0593
application sub category: topic 3292
application sub category: topic 3343
citation: CHEMRXIV.7172369.V2
description: A Crowd-Sourced, Natural Product Screening Library for Exploring Biological Space.
feature list: operation 3435
feature list: operation 3799
feature list: operation 3802

CaptureProbe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0632
application sub category: topic_0634
application sub category: topic_0654
citation: J.ISSN.2095-8137.2020.010
citation: pmcid:PMC6956725
citation: pubmed:31840950
description: A java tool for designing probes for capture Hi-C applications. Here, we developed CaptureProbe, a user-friendly and graphical Java tool for designing capture probes for Capture Hi-C applications. CaptureProbe is easy-to-use, only need simple input files and provides abundant parameters for designing probes. CaptureProbe can design probes specifically for both genomic sites and genomic regions of interest. Comparisons with existing softwares (HiCapTools and GOPHER) indicated that CaptureProbe has a good design success ratio and better probe specificity. Citation: MA Y F, ADEOLA A C, SUN Y B, et al. 2020. CaptureProbe: a java tool for designing probes for capture Hi-C applications. Zool Res [J], 41: 94-96

CardiacPBPK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3300
application sub category: topic 3375
application sub category: topic 3377
citation: J.COMPBIOMED.2019.103484
citation: pubmed:31606584
description: A tool for the prediction and visualization of time-concentration profiles of drugs in heart tissue. Cardiac mechanistic physiologically based pharmacokinetic simulation application. User Interface (ui) application which implements PBPK models. Prediction of drug effect is valuable in terms of both safety and efficacy. physiologically based pharmacokinetic-quantitative system. 1) Download the tar.gz archive from the https: sourceforge.net projects cardiacpbpk files or clone github repository (if you have git packages installed in konsole terminal type ‘git clone https: github.com jszlek CardiacPBPK.git’)
feature list: operation_0337
license: GPL-3.0

CardiacProfileR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0625
application sub category: topic 3318
application sub category: topic 3335
citation: s12551-019-00498-2
citation: pmcid:PMC6381356
citation: pubmed:30666509
description: R package for extraction and visualisation of heart rate profiles from wearable fitness trackers.
feature list: operation_0337
feature list: operation 3436
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Victor Chang Cardiac Research Institute

CardioFAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic 3360
application sub category: topic 3444
citation: S10237-019-01163-Z
citation: pubmed:31076923
description: Platform for noninvasive assessment of pulse transit time and pulsatile flow in hyperelastic vascular networks.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Yashar Seyed Vahedein

Cas-analyzer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic 3168
application sub category: topic 3303
citation: btw561
description: Online tool for assessing genome editing results using NGS data.
feature list: operation_0420
feature list: operation 3096
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Jin-Soo Kim
primary contact: Sangsu Bae

Cascabel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic_0780
application sub category: topic 3168
application sub category: topic 3174
application sub category: topic 3697
citation: https://doi.org/10.1101/809384
description: A flexible, scalable and easy-to-use amplicon sequence data analysis pipeline. CASCABEL is a pipeline designed to run amplicon sequence analysis across single or multiple read libraries. The objective of this pipeline is to create different output files which allow the user to explore data in a simple and meaningful way, as well as facilitate downstream analysis, based on the generated output files.
feature list: operation_0450
feature list: operation 3192
feature list: operation 3200
feature list: operation 3460
license: GPL-3.0

Cassiopeia
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0749
application sub category: topic 2229
citation: https://doi.org/10.1101/800078
citation: s13059-020-02000-8
citation: pmcid:PMC7155257
citation: pubmed:32290857
description: Inference of Single-Cell Phylogenies from Lineage Tracing Data. A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction. This is a software suite for proecessing data from single cell lineage tracing experiments. This suite comes equipped with three main modules:. Phylogeny Reconstruction: a collection of tools for constructing phylogenies. We support 5 algorithms currently: a greedy algorithm based on multi-state compatibility, an exact Steiner-Tree solver, Cassiopeia (the combination of these two), Neighbor-Joining, and Camin-Sokal Maximum Parsimony. Target Site Sequencing Pipeline: a pipeline for extracing lineage information from raw fastqs produced from a lineage tracing experiment
feature list: operation_0326
feature list: operation 3478
feature list: operation 3745
license: MIT

Catalysis Hub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 2258
application sub category: topic 3332
citation: S41597-019-0081-Y
citation: pmcid:PMC6538711
citation: pubmed:31138816
description: Web-platform for sharing data and software for computational catalysis research.
feature list: operation_0384
feature list: operation 3431
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest
software help: about
primary contact: Kirsten Winther
primary contact: Thomas Bligaard

CauseMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3407
application sub category: topic 3577
citation: peerj.preprints.583v2
citation: peerj.824
citation: pmcid:PMC4359046
citation: pubmed:25780776
description: Fast inference of causality from complex time series. Causal inference in non-linear dynamics systems. Welcome to CauseMap — CauseMap 0.1.0 documentation. CauseMap is an implementation of Convergent Cross Mapping (CCM), written in Julia. CauseMap is an implementation of Convergent Cross Mapping (CCM) [1], written in Julia
feature list: operation_0337
feature list: operation 3659
license: MIT

CellAge
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 3399
citation: https://doi.org/10.1101/743781
description: A Multidimensional Systems Biology Analysis of Cellular Senescence in Ageing and Disease | ABSTRACT Cellular senescence, a permanent state of replicative arrest in otherwise proliferating cells, is a hallmark of ageing and has been linked to ageing-related diseases like cancer. Senescent cells have been shown to accumulate in tissues of aged organisms which in turn can lead to chronic inflammation. Many genes have been associated with cell senescence, yet a comprehensive understanding of cell senescence pathways is still lacking. To this end, we created CellAge ( http: genomics.senescence.info cells ), a manually curated database of 279 human genes associated with cellular senescence, and performed various integrative and functional analyses
feature list: operation 2942
feature list: operation 3463
feature list: operation 3501

CellAssign
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
application sub category: topic 2830
application sub category: topic 3170
citation: S41592-019-0529-1
citation: pubmed:31501550
description: Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling | Automated, probabilistic assignment of cell types in scRNA-seq data | cellassign automatically assigns single-cell RNA-seq data to known cell types across thousands of cells accounting for patient and batch specific effects. Information about a priori known markers cell types is provided as input to the model in the form of a (binary) marker gene by cell-type matrix. cellassign then probabilistically assigns each cell to a cell type, removing subjective biases from typical unsupervised clustering workflows
feature list: operation 3431
feature list: operation 3501
feature list: operation 3891

CellBench
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0769
application sub category: topic 3170
citation: BTZ889
citation: pmcid:PMC7141847
citation: pubmed:31778143
description: R/Bioconductor software for comparing single-cell RNA-seq analysis methods. Construct Benchmarks for Single Cell Analysis Methods. This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods
feature list: operation_0244
feature list: operation 3557
feature list: operation 3680
license: GPL-3.0

CellBender
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0099
application sub category: topic_0203
application sub category: topic 3170
citation: https://doi.org/10.1101/791699
description: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets. CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. Welcome to CellBender’s documentation! — CellBender documentation. Free document hosting provided by Read the Docs. Stephen J Fleming, John C Marioni, and Mehrtash Babadi. CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets. bioRxiv 791699; doi: https://doi.org/10.1101/791699.
feature list: operation 2422
feature list: operation 2495
feature list: operation 3799
license: BSD-3-Clause
software help: cellbender.readthedocs.io

CellBin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: We present CellBin, an image-facilitated one-stop pipeline for high-resolution and large field-of-view spatial transcriptomic data of Stereo-seq. CellBin provides a comprehensive and systematic platform for generating high-confidence single-cell spatial gene expression profiles, which specifically includes image stitching, image registration, tissue segmentation, nuclei segmentation and molecule labeling. CellBin is user-friendly and does not require a specific level of omics and image analysis expertise.

CellCountCV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 2229
application sub category: topic 3292
application sub category: topic 3382
application sub category: topic 3474
citation: https://doi.org/10.1101/867218
description: CellCountCV – a web-application for accurate cell counting and automated batch processing of microscopy images using fully-convolutional neural networks. This repository contains the code and examples accompaining our preprint https://doi.org/10.1101/867218. Working_with_CellCounter.ipynb — this notebook contains the examples of pretrained FCNN model usage in Python and through JSON-RPC calls to CellCountCV
feature list: operation 3435
feature list: operation 3443
feature list: operation 3552
license: MIT

CellMinerCDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0208
application sub category: topic 3170
application sub category: topic 3360
citation: j.isci.2019.10.059
citation: 0008-5472.can-18-2047
citation: 0008-5472.can-22-2996
citation: pmcid:PMC10330642
citation: pmcid:PMC6615556
citation: pmcid:PMC6889472
citation: pubmed:31113817
citation: pubmed:31733513
citation: pubmed:37140427
description: Web application for exploration and analysis of cancer cell line pharmacogenomic data across different sources.
feature list: operation_0264
feature list: operation 3501
feature list: operation 3800
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: cellminercdb

CellProfiler
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0625
application sub category: topic 3382
application sub category: topic 3518
citation: cpz1.89
citation: https://doi.org/10.2144/000112257
description: Tool for quantifying data from biological images, particularly in high-throughput experiments.
feature list: operation 1812
feature list: operation 3443
feature list: operation 3799
is accessible for free: true
license: BSD-3-Clause
operating system: Mac
operating system: Windows
software help: index.html

CellSim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3395
citation: s12859-019-2699-3
citation: pmcid:PMC6399906
citation: pubmed:30832570
description: A software aims to calculate the similarity among different cells and predict their co-regulation networks.
feature list: operation 3436
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.1

CellSort
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0749
application sub category: topic 2229
application sub category: topic 3474
citation: btw710
description: Support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort.
feature list: operation 3501
feature list: operation 3660
feature list: operation 3802
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Keith E. J. Tyo

CellTag
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Workflow
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
citation: S13059-019-1699-Y
citation: pmcid:PMC6509836
citation: pubmed:31072405
description: Genetic barcode-based sample multiplexing for single-cell genomics.
feature list: operation 1812
feature list: operation 3200
feature list: operation 3891
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0001-8561-4340

Cell Studio
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0804
application sub category: topic 2229
application sub category: topic 3306
citation: https://doi.org/10.1063/1.5039473
citation: pmcid:PMC6481718
citation: pubmed:31069304
description: Platform for interactive, 3D graphical simulation of immunological processes.
feature list: operation_0337
feature list: operation 2426
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Uri Nevo

Census Travel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0780
application sub category: topic 3305
application sub category: topic 3324
citation: RSTB.2018.0260
citation: pmcid:PMC6558561
citation: pubmed:31104596
description: Probabilistic census-travel model to predict introduction sites of exotic plant, animal and human pathogens.
feature list: operation 3461
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Census Travel
primary contact: https://orcid.org/0000-0003-0885-8004

Cerebro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Library
application sub category: topic_0602
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/631705
description: Software for interactive visualization of scRNA-seq data.
feature list: operation 1812
feature list: operation 3501
is accessible for free: true
license: MIT
operating system: Mac
operating system: Windows

Cgrid
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3444
application sub category: topic 3473
citation: j.jneumeth.2020.108738
citation: https://doi.org/10.1101/786368
citation: pubmed:32305449
description: A toolbox for creating Cartesian Geometric Representations with Isometric Dimensions (Cgrids). The Cgrid-toolbox can be used to generate rectangular representations of brain areas.
feature list: operation_0303
feature list: operation 3357
license: GPL-3.0

ChAsE
type: SoftwareApplication
input: Alignment
  type: FormalParameter
  additional type: data 1916
  encoding format: format 3006
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3173
citation: btw382
citation: cgf.12096
citation: pmcid:PMC5079470
citation: pubmed:27378294
description: ChAsE (Chromatin Analysis and Exploration) is a cross platform desktop application that provides an interactive graphical interface for analysis of epigenomic data. Features include: - Exploration and visualization of the data using an interactive heat map and plot interface - Clustering the data automatically or manually by sorting and brushing the heat map - Exporting results for downstream analysis or as high quality images for publications
feature list: operation_0337
feature list: operation 2451
feature list: operation 3432
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation
software help: README.md
software version: 1.1.2
primary contact: Hamid Younesy

ChEA3
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0749
application sub category: topic 3170
application sub category: topic 3512
citation: GKZ446
citation: pmcid:PMC6602523
citation: pubmed:31114921
description: Transcription factor enrichment analysis by orthogonal omics integration.
feature list: operation 2436
feature list: operation 3463
feature list: operation 3766
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: chea3
primary contact: https://orcid.org/0000-0002-6904-1017

ChIA-PET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3169
application sub category: topic 3179
citation: https://doi.org/10.1101/627257
description: Computational package to process the next-generation sequence data generated from ChIA-PET experiments.
feature list: operation_0443
feature list: operation 3222
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Guoliang Li

ChIPSummitDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3534
citation: https://doi.org/10.1101/652420
description: ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them.
feature list: operation_0445
feature list: operation 2464
feature list: operation 3903
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Documentation.php
software help: Help.php
software help: tutorial.php
primary contact: Endre Barta

ChIPdig
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3295
citation: F1000RESEARCH.20027.1
description: A comprehensive user-friendly tool for mining multi-sample ChIP-seq data | a tool for analysing and mining multi-sample ChIP-seq data | ChIPdig is a tool designed for the bulk analysis of ChIP-seq data comprising multiple samples. Its capabilities are organized into four analysis modules: | In the example above, the first command establishes communication with the Bioconductor repository and the second command installs package “edgeR”. Repeat the second command for the remaining Bioconductor packages used by ChIPdig:
feature list: operation 3192
feature list: operation 3222
feature list: operation 3501
license: GPL-3.0

ChIPseqSpikeInFree
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3169
application sub category: topic 3179
application sub category: topic 3295
citation: BTZ720
citation: pmcid:PMC7523640
citation: pubmed:31566663
description: > CORRECT NAME OF TOOL COULD ALSO BE 'RESULTS:ChIPseqSpikeInFree' | A ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in | A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications | We develop ChIPseqSpikeInFree, a novel ChIP-seq normalization method to effectively determine scaling factors for samples across various conditions and treatments, which does not rely on exogenous spike-in chromatin or peak detection to reveal global changes in histone modification occupancy. This method is capable of revealing the similar magnitude of global changes as the spike-in method | Traditional reads per million (RPM) normalization method is inappropriate for the evaluation of ChIP-seq data when the treatment or mutation has the global effect
feature list: operation 3222
feature list: operation 3501
feature list: operation 3798
license: Apache-2.0

ChIPulate
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3179
citation: journal.pcbi.1006921
citation: pmcid:PMC6445533
citation: pubmed:30897079
description: A Python3 framework to simulate read counts in a ChIP-seq experiment.
feature list: operation_0308
feature list: operation_0445
feature list: operation 3222
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Vishaka Datta S

ChaRTr
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
citation: J.JNEUMETH.2019.108432
citation: pmcid:PMC6980795
citation: pubmed:31586868
description: An R toolbox for modeling choices and response times in decision-making tasks. BACKGROUND:Decision-making is the process of choosing and performing actions in response to sensory cues to achieve behavioral goals. Many mathematical models have been developed to describe the choice behavior and response time (RT) distributions of observers performing decision-making tasks. However, relatively few researchers use these models because it demands expertise in various numerical, statistical, and software techniques. NEW METHOD:We present a toolbox - Choices and Response Times in R, or ChaRTr - that provides the user the ability to implement and test a wide variety of decision-making models ranging from classic through to modern versions of the diffusion decision model, to models with urgency signals, or collapsing boundaries.
feature list: operation 2426
feature list: operation 3799

ChaperISM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0749
citation: BTZ670
citation: pubmed:31504177
description: improved chaperone binding prediction using position-independent scoring matrices | ChaperISM is an algorithm to identify Hsp70 binding sequences in proteins. It uses a position-independent scoring matrix which was trained on either qualitative or quantitative chemiluminescence data previously published, obtained from interaction between DnaK and different ligands. Both versions of ChaperISM, qualitative or quantitative, resulted in an improved performance in comparison to other state-of-the-art chaperone binding predictors
feature list: operation 2492
feature list: operation 3799

ChemAGG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3336
application sub category: topic 3373
citation: ACS.JCIM.9B00541
citation: pubmed:31430151
description: Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery | Aggregator Prediction-Webserver-ADMElab | Aggregation is one of the main reasons of false positives in HTS. To build a reliable prediction model, we collected a large dataset of aggregators and drugs to build several models based on the combination of different descriptors and algorithm, ChemAGG is a free webserver that could be used to easily filter out aggregators from potential lead molecules!
feature list: operation 3216
feature list: operation 3436

ChemDataExtractor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0593
application sub category: topic 2258
application sub category: topic 3316
application sub category: topic 3489
citation: S41597-019-0306-0
citation: pmcid:PMC6895184
citation: pubmed:31804487
description: Comparative dataset of experimental and computational attributes of UV/vis absorption spectra. ChemDataExtractor toolkit tailored towards UV/vis absorption spectroscopy peak data. ChemDataExtractor toolkit tailored towards UV/vis absorption spectroscopy peak data. This work adapts the underlying table extraction mechanics of ChemDataExtractor version 1.3 , for higher precision extraction of maximum absorption peak wavelength data and associated extinction coefficients.
feature list: operation_0224
feature list: operation_0306
feature list: operation_0399
license: MIT
software help: intro

ChemEnv
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: s2052520620007994
citation: pmcid:PMC7412753
citation: pubmed:32831287
description: A Fast and Robust Coordination Environment Identification Tool. Coordination or local environments have been used to describe, analyze, and understand crystal structures for more than a century. Here, we present a new tool called ChemEnv< i>, which can identify coordination environments in a fast and robust manner. In contrast to previous tools, the assessment of the coordination environments is not biased by small distortions of the crystal structure. Its robust and fast implementation enables the analysis of large databases of structures. The code is available open source within the pymatgen< i> package and the software can as well be used through a web app available on http: crystaltoolkit.org through the Materials Project.

ChemPager
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3314
citation: CHIMIA.2019.724
citation: pubmed:31514773
description: ChemPager is a freely available data analysis tool for analyzing, comparing and improving synthetic routes. Functions include prediction of the cumulative process mass intensity of chemical routes, irrespective of their development status, by comparison with a set of reactions executed on large scale. Along with the prediction of this core green chemistry metric aims to improve existing routes and help the decision-making process among route alternatives without the need for experimental data.
license: MIT

ChemSuite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2258
application sub category: topic 3474
citation: cbdd.13479
citation: pubmed:30637953
description: Package for chemoinformatics calculations and machine learning.
feature list: operation 2945
feature list: operation 3438
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

ChiCMaxima
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3173
citation: s13059-019-1706-3
citation: pmcid:PMC6532271
citation: pubmed:31118054
description: Pipeline for analyzing and identificantion of chromation loops in CHi-C promoters data.
feature list: operation_0337
feature list: operation 3501
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Readme.pdf
primary contact: T. Sexton
primary contact: Y. Ben Zouari

Chi.Bio
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0632
application sub category: topic 3070
application sub category: topic 3361
citation: https://doi.org/10.1101/796516
description: An open-source automated experimental platform for biological science research. By combining heating, stirring, liquid handling, spectrometry, and optogenetics into a single easy-to-use platform, Chi.Bio can simplify laboratory protocols and drastically reduce equipment costs. No more will tired graduate students need to stay late in the lab to induce experiments, or run samples between incubators and plate readers.
feature list: operation 3891

ChickpeaMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: A mine with chickpea data (both desi and kabuli varieties) from the Legume Information Systems (LIS) tripal.chado database
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 0.10

Chickspress
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3500
application sub category: topic 3810
citation: baz058
citation: pmcid:PMC6556980
citation: pubmed:31210271
description: Chickspress Genome Browser.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Eric H Lyons
primary contact: Fiona M McCarthy
primary contact: Shane C Burgess

Chipper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3382
application sub category: topic 3489
application sub category: topic 3500
citation: https://doi.org/10.1101/807974
citation: 2041-210X.13368
description: Open-source software for semi-automated segmentation and analysis of birdsong and other natural sounds. Abstract Audio recording devices have changed significantly over the last 50 years, making large datasets of recordings of natural sounds, such as birdsong, easier to obtain. This increase in digital recordings necessitates an increase in high-throughput methods of analysis for researchers. Specifically, there is a need in the community for open-source methods that are tailored to recordings of varying qualities and from multiple species collected in nature. We developed Chipper, a Python-based software to semi-automate both the segmentation of acoustic signals and the subsequent analysis of their frequencies and durations.
feature list: operation 2422
feature list: operation 3435
feature list: operation 3891

ChlamDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0797
application sub category: topic 3293
application sub category: topic 3489
citation: GKZ924
citation: pmcid:PMC7145651
citation: pubmed:31665454
description: A comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum. ChlamDB documentation — ChlamDB 2.0 (June 2019) documentation. A comparative genomics database of the phylum Chlamydiae and other PVC (Planctomycetes, Verrucomicrobia, Lentisphaerae). Problems and errors encountered on the ChlamDB website can be announced on the github page of the website
feature list: operation_0303
feature list: operation 2421
feature list: operation 2422
software help: index.html

Chordomics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0121
application sub category: topic 3697
citation: BTZ711
citation: pubmed:31539022
description: A visualisation tool for linking function to phylogeny in microbiomes | Interactive visualisation and data annotation for meta-omics data | Chordomics is a tool to visualize and interpret linked data, such as from metagenomics or metaproteomics where both taxonomic and functional data is obtained | The demonstration version of Chordomics is available at https://kmcd.shinyapps.io/chordomics/. Here, a toy dataset is provided to allow you to see the explorative capabilities Chordomics provides before you need to install it!
feature list: operation_0337
feature list: operation 1812
license: MIT

ChromDragoNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic 3474
citation: BTZ352
citation: pmcid:PMC6612838
citation: pubmed:31510655
description: Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts | Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts" | ChromDragoNN: cis-trans Deep RegulAtory Genomic Neural Network for predicting Chromatin Accessibility
feature list: operation_0441
feature list: operation 3192
feature list: operation 3439
license: MIT

ChromaClade
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0749
application sub category: topic 2815
application sub category: topic 3293
citation: S12862-019-1518-9
citation: pmcid:PMC6792252
citation: pubmed:31615393
description: A combined visualisation of phylogenetic and sequence data. Combined visualisation of phylogenetic and sequence data. Please see 'release' tab for executables and documentation below. ChromaClade is a desktop bioinformatics application that produces visualisations combining sequence and phylogenetic data. It annotates taxon names in a phylogenetic tree with amino acids found at individual sites in a corresponding sequence alignment. Residue-specific colour codes enable easy inspection by eye and the resulting trees can be viewed in any of several popular tree-viewing programs
feature list: operation_0558
feature list: operation_0564
feature list: operation_0567
license: Apache-2.0

Chromatiblock
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0622
application sub category: topic_0798
application sub category: topic 3382
citation: https://doi.org/10.1101/800920
citation: joss.02451
description: A scalable whole-genome visualization of structural differences in prokaryotes. Colinear block visualisation tool. To create a fresh environment for chromatiblock to run in do:. Scalable, whole-genome visualisation of structural changes in prokaryotes. Will run chromatiblock on all fasta or genbank files in /path/to/fasta_directory/ and create an interactive webpage of the output. Intermediate files will be created in cb_working_dir
feature list: operation_0337
feature list: operation_0496
feature list: operation 3840
license: GPL-3.0

CiDD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 3336
citation: 1535-7163.MCT-14-0260
citation: pmcid:PMC4341901
citation: pubmed:25349306
description: Cancer in silico Drug Discovery (CIDD) is a platform to integrate data from the TCGA, Connectivity Map (CMap) and Cancer Cell Line Encyclopedia to facilitate and automate discovery of candidate drug compounds with the ultimate goal for treatment or chemo-prevention of cancer.
feature list: operation 2495
feature list: operation 3223
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: cidd
primary contact: Paul Scheet

CiiiDER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0204
application sub category: topic_0749
application sub category: topic 3308
citation: JOURNAL.PONE.0215495
citation: pmcid:PMC6726224
citation: pubmed:31483836
description: A tool for predicting and analysing transcription factor binding sites | CIIIDER is a user-friendly tool for predicting and analysing transcription factor binding sites, designed with biologists in mind | Transcription factor binding site prediction and visualisation software
feature list: operation_0420
feature list: operation_0445
feature list: operation 2464

CiliaCarta
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0625
application sub category: topic 3676
citation: JOURNAL.PONE.0216705
citation: pmcid:PMC6522010
citation: pubmed:31095607
description: An integrated and validated compendium of ciliary genes.
feature list: operation 3501
feature list: operation 3629
feature list: operation 3638
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: 0000-0002-8122-190X
primary contact: Martijn A. Huynen

Ciona robusta Anatomy and Development Ontology
type: SoftwareApplication
input: Bibliography
  type: FormalParameter
  additional type: data 3505
  encoding format: format 2330
output: Ontology concept ID
  type: FormalParameter
  additional type: data 1087
  encoding format: format 2196
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Ontology
application sub category: topic 3064
citation: gkv966
citation: gr.108175.110
description: The first ontology describing the anatomy and the development of Ciona robusta, based on the Hotta developmental table.
feature list: operation_0226
feature list: operation_0335
is accessible for free: true
license: Freeware

Circular Gene Ontology (CirGO)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0089
application sub category: topic_0092
application sub category: topic_0203
citation: s12859-019-2671-2
citation: pmcid:PMC6380029
citation: pubmed:30777018
description: Visualises non-redundant two-level hierarchically structured ontology terms from gene expression data in a 2D space.
feature list: operation_0570
feature list: operation 2942
feature list: operation 3559
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Artur Lugmayr
primary contact: Irina Kuznetsova

CircCode
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 2229
application sub category: topic 3512
citation: FGENE.2019.00981
citation: pmcid:PMC6795751
citation: pubmed:31649739
description: A Powerful Tool for Identifying circRNA Coding Ability. A Python3-base pipeline for translated circular RNA(circRNA) identification. CircCode is a Python3-base pipeline for translated circular RNA identification. It automatically tandem links sequence in series and processes a given ribosome profile data (including quality control, filtering and alignment). Finally, based on random forest and J48 classification, the final translated circular RNA was predicted. The user only needs to fill in the given configuration file and run the python scripts to get the predicted translated circular RNA
feature list: operation_0436
feature list: operation_0570
feature list: operation 3695
license: GPL-3.0

CircFunBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
additional type: Web application
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 3512
author: Dahui Hu
author: Ming Chen
author: Xianwen Meng
citation: baz003
citation: pmcid:PMC6360206
citation: pubmed:30715276
description: Database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions.
feature list: operation 2422
feature list: operation 3431
feature list: operation 3501
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
primary contact: Ming Chen

CircPro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3512
citation: btx446
citation: pubmed:29028266
description: Integrated tool for the identification of circRNAs with protein-coding potential.
feature list: operation_0436
feature list: operation 2495
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: manual.pdf
primary contact: Ming Chen
primary contact: Xianwen Meng

CircRiC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3512
citation: S13073-019-0663-5
citation: pmcid:PMC6709551
citation: pubmed:31446897
description: Comprehensive characterization of circular RNAs in ~ 1000 human cancer cell lines | The CircRic refers to “circular RNA in cancers”. Circular RNAs (circRNAs) is class of non-coding RNA generated in a “back-splicing”. Recent studies have highlighted the important role of circRNAs in cancer. Here, we systematically characterize circRNAs expression profile in 935 cancer cell lines across 22 cancer lineages from Cancer Cell line Encyclopedia (CCLE), and analyzed the circRNAs biogenesis regulators, effect of circRNAs on drug response and association between circRNAs with mRNA, protein and mutation, and predicted RNA regulatory element in circRNAs
feature list: operation_0441
feature list: operation_0443
feature list: operation 2495

CircaCompare
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 3070
citation: BTZ730
citation: pubmed:31588519
description: A method to estimate and statistically support differences in mesor, amplitude, and phase, between circadian rhythms. circacompare is an R package that allows for the statistical analyses and comparison of two circadian rhythms. This work is published here and can be cited as:. Rex Parsons, Richard Parsons, Nicholas Garner, Henrik Oster, Oliver Rawashdeh, CircaCompare: A method to estimate and statistically support differences in mesor, amplitude, and phase, between circadian rhythms, Bioinformatics, https://doi.org/10.1093/bioinformatics/btz730
feature list: operation_0337
feature list: operation 3454
feature list: operation 3659

Circle-Map
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0654
application sub category: topic 3168
citation: S12859-019-3160-3
citation: pmcid:PMC6909605
citation: pubmed:31830908
description: Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads. A method for circular DNA detection based on probabilistic mapping of ultrashort reads. Welcome to Circle-Map official repository!. Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. The package contains easy to run algorithms for accurately detect circular DNA formed from mappable and non mappable regions of a genome.
feature list: operation 3198
feature list: operation 3227
feature list: operation 3435
license: MIT

Cistrome-GO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
additional type: Web service
application sub category: topic_0204
application sub category: topic_0749
application sub category: topic 3169
citation: GKZ332
citation: pmcid:PMC6602521
citation: pubmed:31053864
description: Web server for functional enrichment analysis of transcription factor ChIP-seq peaks.
feature list: operation 3222
feature list: operation 3223
feature list: operation 3501
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: Tutorial.html
primary contact: Clifford A Meyer
primary contact: X Shirley Liu

CiteFuse
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: btaa282
citation: https://doi.org/10.1101/854299
citation: pubmed:32353146
description: CiteFuse enables multi-modal analysis of CITE-seq data. multi-modal analysis of CITE-seq data. CiteFuse is a streamlined package consisting of a suite of tools for pre-processing, modality integration, clustering, differential RNA and ADT expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualization of CITE-seq data
feature list: operation_0337
feature list: operation 2495
feature list: operation 3799

CladePP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3053
application sub category: topic 3293
citation: gr.241414.118
citation: pmcid:PMC6396423
citation: pubmed:30718334
description: Clade Phylogenetic Profiling (CladePP) detects local coevolution across hundreds of genomes and points to the evolutionary scale (e.g. mammals, vertebrates, animals, plants) at which coevolution occurred.
feature list: operation_0533
feature list: operation 3501
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: D. Rahat

Clair
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic 3047
application sub category: topic 3295
application sub category: topic 3474
citation: s42256-020-0167-4
citation: https://doi.org/10.1101/865782
description: Exploring the limit of using a deep neural network on pileup data for germline variant calling. Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling. Clair - Yet another deep neural network based variant caller. Single-molecule sequencing technologies have emerged in recent years and revolutionized structural variant calling, complex genome assembly, and epigenetic mark detection
feature list: operation_0525
feature list: operation 3196
feature list: operation 3227
license: BSD-3-Clause

ClassifyMe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3382
application sub category: topic 3474
application sub category: topic 3500
citation: https://doi.org/10.1101/646737
description: Field-scouting software for the identification of wildlife in camera trap images.
feature list: operation 3435
feature list: operation 3891
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

ClassyFire
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic_0089
application sub category: topic_0154
application sub category: topic_0637
application sub category: topic 2258
application sub category: topic 3314
citation: C9EM00321E
citation: pubmed:31576380
description: A webapplication for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy.
feature list: operation 2422
feature list: operation 2996
feature list: operation 3359

ClickGene
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3517
citation: S13040-019-0202-3
citation: pmcid:PMC6595587
citation: pubmed:31391866
description: An open cloud-based platform for big pan-cancer data genome-wide association study, visualization and exploration | Click: Do GWAS analysis by yourself by Clicking | More than 30 cancer types, more than 10,000 samples | Including gene expression, copy number variation, methylation and mutation data categories | You are accessing a non-profit web site which is based on GDC data portal hosted by National Cancer Institute, USA. All data was downloaded from GDC public database. Please make sure you are aware of and obey the policy of GDC data portal. Please go to User`s Guide for more information | Beeswarm plot, Manhattan plot, Volcano plot, Mountain plot, Deflection plot, Linear regression analysis, significance test and
feature list: operation_0337
feature list: operation 3659
software help: guide

ClinCNV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0621
application sub category: topic 2269
application sub category: topic 3518
application sub category: topic 3673
application sub category: topic 3676
citation: https://doi.org/10.1101/837971
description: A novel method for allele-specific somatic copy-number alterations detection. Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data. A tool for large-scale CNV and CNA detection.
feature list: operation_0452
feature list: operation 3227
feature list: operation 3435
license: MIT

ClinEpiDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0621
application sub category: topic 3305
application sub category: topic 3324
application sub category: topic 3382
citation: GATESOPENRES.13087.1
citation: gatesopenres.13087.2
description: An open-access clinical epidemiology database resource encouraging online exploration of complex studies. The concept of open data has been gaining traction as a mechanism to increase data use, ensure that data are preserved over time, and accelerate discovery. While epidemiology data sets are increasingly deposited in databases and repositories, barriers to access still remain. ClinEpiDB was constructed as an open-access online resource for clinical and epidemiologic studies by leveraging the extensive web toolkit and infrastructure of the Eukaryotic Pathogen Database Resources (EuPathDB; a collection of databases covering 170+ eukaryotic pathogens, relevant related species, and select hosts) combined with a unified semantic web framework. Here we present an intuitive point-and-click website that allows users to visualize and subset data directly in the ClinEpiDB browser and immediately explore potential associations
feature list: operation_0337
feature list: operation 2421
feature list: operation 3431
license: GPL-2.0

ClinOmicsTrail
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0208
application sub category: topic 2640
application sub category: topic 3400
description: Visual analytics tool for breast cancer treatment stratification.
feature list: operation 3196
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://clinomicstrail.bioinf.uni-sb.de/help

ClinOmicsTrailbc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0208
application sub category: topic 2640
application sub category: topic 3400
citation: btz302
citation: pmcid:PMC6954665
citation: pubmed:31038669
description: Visual analytics tool for breast cancer treatment stratification.
feature list: operation 3196
feature list: operation 3501
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://clinomicstrail.bioinf.uni-sb.de/help

ClinPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 3325
application sub category: topic 3676
citation: j.ajhg.2018.08.005
citation: pmcid:PMC6174354
citation: pubmed:30220433
description: Efficient tool for identifying disease-relevant nonsynonymous single nucleotide variants.
feature list: operation 3196
feature list: operation 3227
feature list: operation 3461
primary contact: Jacek Majewski
primary contact: Najmeh Alirezaie

ClinTAD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic_0749
citation: s10038-019-0573-9
citation: pubmed:30765865
description: Quick evaluation of the clinical relevance of copy number variants (CNVs) in the context of topologically associated domains (TADs).
feature list: operation 3196
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: ClinTAD

ClinVAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic_0769
application sub category: topic 2640
application sub category: topic 3168
citation: btz924
citation: pmcid:PMC7141851
citation: pubmed:31830259
description: Clinical Variant Annotation Pipeline (ClinVAP) creates a genetic report of somatic mutations from a variant call format (VCF) file. Please refer this document for implementation of the pipeline. Documentation of the pipeline is available at Wiki page.
feature list: operation_0310
feature list: operation_0331
feature list: operation_0337
feature list: operation 3226
feature list: operation 3227
license: MIT

CliqueMS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3520
citation: btz207
citation: pmcid:PMC6792096
citation: pubmed:30903689
description: Computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network.
feature list: operation 3798
feature list: operation 3803
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: annotate features.Rmd
software version: 0.3.2
primary contact: Oriol Senan

Clirc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3512
application sub category: topic 3794
citation: PREPRINTS201911.0202.V1
citation: genes11010054
citation: pmcid:PMC7016857
citation: pubmed:31947823
description: Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. Clirc: a user-friendly bioinformatics software to identify RBP-bound circRNAs through analysis of CLIP-Seq data. The Clirc software is designed to identify RBP-bound circRNAs in CLIP-Seq data. The Clirc software internally calls the gsnap aligner for alignment of CLIP-Seq reads. The CLIP-Seq technology comprises of three variants: HITS-CLIP, PAR-CLIP, and iCLIP. The Clirc software works on all three versions of them. It can also work on any type of RNA-Seq data in general, although non-polyA selected RNA-Seq is preferred. The Clirc software is designed to search for known circRNAs in high-throughput sequencing data whose coordinates are provided by users. The users can collect these coordinates from previous publication or their own search using RNA-Seq data. This avoids the common problem of short sequncing reads in CLIP-Seq data. But this approach cannot identify novel circRNAs in CLIP-Seq data
feature list: operation 2495
feature list: operation 3192
feature list: operation 3198

ClonalTREE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0199
application sub category: topic 3168
citation: https://doi.org/10.1101/832063
citation: s12864-019-6328-3
citation: pmcid:PMC6936074
citation: pubmed:31888455
description: Clonal reconstruction from time course genomic sequencing data. ClonalTREE (Clonal reconstruction in Time couRse long-term Evolution Experiment). Usage: python3 ClonalTREE.py <VAF file> <algorithm> <fail threshold> <out prefix> <clones (optional)>
feature list: operation_0487
feature list: operation 3196
feature list: operation 3226
license: GPL-3.0

CluMSID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3520
citation: btz005
citation: pubmed:30649189
description: R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics.
feature list: operation_0337
feature list: operation 3627
feature list: operation 3803
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Tobias Depke

ClustalW2 Phylogeny API EBI
type: SoftwareApplication
input: Sequence alignment
  type: FormalParameter
  additional type: data_0863
output: Phylogenetic tree
  type: FormalParameter
  additional type: data_0872
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0080
application sub category: topic 3293
citation: btm404
citation: pubmed:17846036
description: Create Neighbor-joining or UPGMA phylogentic trees from a multiple sequence alignment using ClustalW.
feature list: operation_0323
operating system: Linux
operating system: Mac
operating system: Windows
software help: clustalw2 phylogeny rest
software version: 1

ClusterBootstrap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
citation: s13428-019-01252-y
citation: pmcid:PMC7148287
citation: pubmed:31089956
description: R package for the analysis of hierarchical data using generalized linear models with the cluster bootstrap.
feature list: operation_0552
feature list: operation 3432
feature list: operation 3659
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ClusterBootstrap
software version: 1.0.0

ClusterBurden
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0634
application sub category: topic 3305
application sub category: topic 3512
application sub category: topic 3676
citation: https://doi.org/10.1101/826164
citation: jmedgenet-2020-106922
citation: pmcid:PMC8327322
citation: pubmed:32732227
description: Enhanced prediction of gene and missense rare-variant pathogenicity by joint analysis of gene burden and amino-acid residue position. Rare variant association using position and burden signals. This method is designed for case-control studies where the condition under investigation is caused by rare variants in protein-coding regions. This is the case for most Mendelian diseases and therefore this method is relevant for these
feature list: operation 2454
feature list: operation 3225
feature list: operation 3461
feature list: operation 3791

ClusterScan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0622
citation: bty486
citation: pubmed:29912285
description: ClusterScan is a tool to search for genomic clusters starting from genomic feature locations and their annotations. It allows the user to scan an annotation file (BED format with locations of specific features such as gene, transcripts, regulatory regions or anything that can be mapped on a genome) and get clusters coordinates in output. In order to build annotated clusters, ClusterScan needs an additional two-columns file, storing the feature ids and the corresponding categorical information (such as Gene Ontology classes, KEGG, Pfam accessions, etc).
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
software help: ClusterScan-Installation
software help: ClusterScan-Tutorial

CmPIweb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
citation: biecoll-jib-2016-298
citation: pubmed:28187414
description: The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybrid-dimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies – Three.js, D3.js and PHP – as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org.

CoBAMP
type: SoftwareApplication
input: Pathway or network
  type: FormalParameter
  additional type: data 2600
  encoding format: format 2585
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
additional type: Script
application sub category: topic_0092
application sub category: topic_0602
application sub category: topic 2259
application sub category: topic 3070
citation: btz598
citation: pubmed:31359031
description: CoBAMP (Constraint-Based Analysis of Metabolic Pathways) is a Python package containing pathway analysis methods for use with constraint-based metabolic models. The main purpose is to provide a framework that is both modular and flexible enough to be integrated in other packages (such as cobrapy, framed or cameo) that already implement generic data structures for metabolic models.
feature list: operation 3439
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: modules.html
software help: quickstart.html
software version: 0.1.4
primary contact: https://orcid.org/0000-0001-9604-9586

CoCo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3512
citation: btz433
citation: pmcid:PMC6901076
citation: pubmed:31141144
description: Count Corrector for nested genes and multi-mapped reads.
feature list: operation 3563
feature list: operation 3798
feature list: operation 3800
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: MANUAL.md
software help: README.md

CoDReS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2258
application sub category: topic 3336
application sub category: topic 3379
citation: J.CSBJ.2019.05.010
citation: pmcid:PMC6637175
citation: pubmed:31360332
description: A Web Tool for Ranking Candidate Drugs Against a Selected Disease Based on a Combination of Functional and Structural Criteria | Computational Drug Repositioning Score

CoExpresso
type: SoftwareApplication
input: UniProt accession
  type: FormalParameter
  additional type: data 3021
  encoding format: format 1963
input: Gene ID
  type: FormalParameter
  additional type: data 2295
  encoding format: format 1963
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 3508
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0092
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic 2269
application sub category: topic 3520
citation: s12859-018-2573-8
citation: pmcid:PMC6327379
citation: pubmed:30626316
description: CoExpresso is a tool to investigate the behavior of protein subunits in known complexes by comparing their abundance profiles across up to 140 cell types available in ProteomicsDB. Thorough assessment of different randomization methods and statistical scoring algorithms allows determining the significance of concurrent profiles within a complex, therefore providing insights into the conservation of their composition across human cell types as well as the identification of intrinsic structures in complex behavior to determine which proteins orchestrate complex function.
feature list: operation_0224
feature list: operation_0276
feature list: operation_0531
feature list: operation_0571
feature list: operation 2238
feature list: operation 2495
feature list: operation 2935
feature list: operation 3083
feature list: operation 3463
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: coexpresso
primary contact: Veit Schwämmle

CoMM-S
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2269
application sub category: topic 3517
citation: https://doi.org/10.1101/652263
description: Collaborative mixed model to dissecting genetic contributions to complex traits by leveraging regulatory information.
feature list: operation 3196
feature list: operation 3232
feature list: operation 3557
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Jin Liu

CoMW
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0196
application sub category: topic 3308
application sub category: topic 3512
citation: https://doi.org/10.1101/642348
description: Comparative Metatranscriptomics Workflow is a standardized and validated workflow to functionally classify quality filtered mRNA reads from metatranscriptomic or total RNA studies generated using NGS short reads.
feature list: operation_0524
feature list: operation 2495
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: CoMW Manual.pdf
primary contact: Carsten Suhr Jacobsen
primary contact: Muhammad Zohaib Anwar

CoMetGeNe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3407
author: Alexandra Zaharia
citation: s12859-018-2542-2
citation: pmcid:PMC6327494
citation: pubmed:30630411
description: CoMetGeNe (COnserved METabolic and GEnomic NEighborhoods) - exploration tool for conserved organizational motifs at both the metabolic and genomic level.
feature list: operation 3660
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: manual.html
software help: CoMetGeNe
primary contact: Alexandra Zaharia

CoNekT-Plants
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0780
citation: https://doi.org/10.1101/744326
citation: tpc.19.00780
citation: pubmed:31988262
description: Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and roots | A platform dedicated to the visualization and analysis of plant co-expression and co-function networks
feature list: operation_0313
feature list: operation 3463
feature list: operation 3766

CoPhosK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3520
author: Marzieh Ayati
author: Mehmet Koyuturk
citation: journal.pcbi.1006678
citation: pmcid:PMC6411229
citation: pubmed:30811403
description: Method for Co-phosphorylation-based Kinase-substrate interaction prediction (CophosK).
feature list: operation_0417
feature list: operation 3501
feature list: operation 3639
is accessible for free: true
operating system: Linux
operating system: Mac
primary contact: Mark R. Chance
primary contact: Marzieh Ayati

CoRNeA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic 3957
citation: https://doi.org/10.1101/741280
citation: biom10060938
citation: pmcid:PMC7356028
citation: pubmed:32580303
description: A pipeline to decrypt the inter protein interfaces from amino acid sequence information | Abstract Computational methods have been devised in the past to predict the interface residues using amino acid sequence information but have been majorly applied to predict for prokaryotic protein complexes. Since the composition and rate of evolution of the primary sequence are different between prokaryotes and eukaryotes, it is important to develop a method specifically for eukaryotic complexes. Here we report a new hybrid pipeline for the prediction of protein-protein interaction interfaces from the amino acid sequence information alone based on the framework of Co -evolution, machine learning ( R andom forest) and Ne twork A nalysis named CoRNeA trained specifically on eukaryotic protein complexes
feature list: operation_0272
feature list: operation_0303
feature list: operation 2492

CoSIMS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0593
application sub category: topic 3520
citation: acs.jpcb.9b01018
citation: pmcid:PMC6958516
citation: pubmed:31042389
description: Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry.
feature list: operation_0244
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: cosims manual.pdf
primary contact: Alan A. Chen

Cocoa Genome Hub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0203
application sub category: topic_0621
application sub category: topic 3308
application sub category: topic 3810
citation: ng.736
citation: s12864-017-4120-9
citation: pmcid:PMC5603072
citation: pubmed:21186351
citation: pubmed:28915793
contributor: https://orcid.org/0000-0001-6411-7310
description: The Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources.
feature list: operation_0292
feature list: operation 3184
feature list: operation 3559
funder: ANR
is accessible for free: true
license: GPL-2.0
operating system: Linux
software help: 3.x
software help: terms-service
primary contact: https://orcid.org/0000-0002-0100-5511
primary contact: https://orcid.org/0000-0003-1849-1269

CodAn
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0621
application sub category: topic_0780
application sub category: topic 3168
application sub category: topic 3512
citation: https://doi.org/10.1101/794107
description: predictive models for the characterization of mRNA transcripts in Eukaryotes. CodAn (Coding sequence Annotator) is a computational tool designed to characterize the CDS and UTR regions on transcripts from any Eukaryote species
feature list: operation_0278
feature list: operation_0436
feature list: operation_0524
feature list: operation 3800
license: GPL-3.0

CodataGS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0602
application sub category: topic 2885
citation: https://doi.org/10.1101/636746
description: Computes genomic breeding values using external information on the markers. The package fits a linear mixed model with heteroscedastic random effects, where the random effect variance is fitted using a linear predictor and a log link.
feature list: operation_0282
feature list: operation_0488
feature list: operation 3196
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: CodataGS.pdf
primary contact: E. F. Mouresan
primary contact: Lars Ronnegard

Coding Sequence Optimization for Chlamydomonas reinhardtii
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0091
application sub category: topic_0203
application sub category: topic_0780
description: Coding Sequence optimization for Chlamydomonas reinhardtii
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 2.0.0.0
primary contact: Iddo Weiner

Codonome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0204
application sub category: topic 3512
citation: j.ygeno.2013.02.009
citation: pubmed:23466472
description: CODONOME collects the expression value of each codon (just called "codonome") and of each aminoacyl-tRNA synthetase (aaRS). To do this, the software is able to count the total mRNA codon number of any organism and to import and integrate any mRNA expression data source in tabulated text format.
operating system: Mac
operating system: Windows
software help: CODONOME Guide.html

Coffee Genome Hub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0091
application sub category: topic_0780
author: Alexis Dereeper
author: Gaetan Droc
citation: gku1108
citation: science.1255274
citation: pmcid:PMC4383925
citation: pubmed:25190796
citation: pubmed:25392413
description: The Coffee Genome Hub is an integrated web-based database providing centralized access to coffee community genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied research in coffee.
feature list: operation_0361
feature list: operation_0564
is accessible for free: true
license: GPL-2.0
software help: documentation

Coinfinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0621
application sub category: topic_0623
citation: mgen.0.000338
citation: https://doi.org/10.1101/859371
citation: pmcid:PMC7200068
citation: pubmed:32100706
description: Detecting Significant Associations and Dissociations in Pangenomes. A tool for the identification of coincident (associating and dissociating) genes in pangenomes. input/output files associated with the analysis performed in the manuscript describing coinfinder. Coinfinder is an algorithm and software tool that detects genes which associate and dissociate with other genes more often than expected by chance in pangenomes. Coinfinder is written primarily in C++ and is a command line tool which generates text, gexf, and pdf outputs for the user. Written in collaboration with Martin Rusilowicz
feature list: operation 2238
feature list: operation 2422
feature list: operation 3695
license: GPL-3.0

ColiCoords
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3316
application sub category: topic 3382
citation: journal.pone.0217524
citation: pubmed:31216308
description: Python package for the analysis of bacterial fluorescence microscopy data.
feature list: operation 3431
feature list: operation 3443
feature list: operation 3552
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest
primary contact: J. H. Smit

CollaboNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic 3474
citation: S12859-019-2813-6
citation: pmcid:PMC6538547
citation: pubmed:31138109
description: Collaboration of deep neural networks for biomedical named entity recognition.
feature list: operation 3280
feature list: operation 3625
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Jaewoo Kang

Collector
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
additional type: Web service
application sub category: topic_0089
application sub category: topic_0202
application sub category: topic_0209
citation: btx566
citation: pubmed:28968713
description: Tool that allows extracting from the Open PHACTS Discovery platform series of compounds annotated with experimental data that can be used directly for building QSAR predictive models.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Collector Setup and user manual v1.5.0.pdf
software help: Collector readme & quickstart v1.5.0.pdf
software help: README.md
primary contact: Manuel Pastor
primary contact: Oriol L. Massaguer

ColocML
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3382
application sub category: topic 3474
application sub category: topic 3520
citation: BTAA085
citation: https://doi.org/10.1101/758425
citation: pmcid:PMC7214035
citation: pubmed:32049317
description: artificial intelligence approach to quantify co-localization between mass spectrometry images | Methods for measuring co-localization of ion images | Measuring co-localization of ion images | This repository is devoted to a project on measuring co-localization of mass spectrometry images. The project is carried out by the Alexandrov team at EMBL Heidelberg. We created a webapp for ranking pairs of ion images, engaged external experts to rank images from their public data from METASPACE, consolidated the results into a gold standard set of ranked pairs of ion images, and, finally, developed and evaluated various measures of co-localization | Katja Ovchinnikova: pixel-based co-localization method development, gold standard preparation
feature list: operation 3891
license: Apache-2.0

ColonySizeDistributions
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0749
application sub category: topic 2640
application sub category: topic 3382
citation: journal.pone.0209591
citation: pmcid:PMC6307751
citation: pubmed:30589908
description: Software tool for the quantification of metastatic colony growth dynamics and size distributions in vitro and in vivo.
feature list: operation 3443
feature list: operation 3795
feature list: operation 3799
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://github.com/sbhoyar1/ColonySizeDistributions/blob/master/Readme.docx
software help: https://github.com/sbhoyar1/ColonySizeDistributions/blob/master/Tutorial.docx

ComHub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3512
citation: https://doi.org/10.1101/840959
description: Community predictions of hubs in gene regulatory networks. Abstract Summary Hub transcription factors, regulating many target genes in gene regulatory networks (GRNs), play important roles as disease regulators and potential drug targets. However, while numerous methods have been developed to predict individual regulator-gene interactions from gene expression data, few methods focus on inferring these hubs. We have developed ComHub, a tool to predict hubs in GRNs. ComHub makes a community prediction of hubs by averaging over predictions by a compendium of network inference methods. Benchmarking ComHub to the DREAM5 challenge data and an independent data set of human gene expression, proved a robust performance of ComHub over all data sets. Lastly, we implemented ComHub to work with both predefined networks and to do standard network inference, which we believe will make it generally applicable
feature list: operation 1781
feature list: operation 2454
feature list: operation 3439

ComParaLogS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0085
application sub category: topic_0780
citation: s12859-018-2420-y
citation: pmcid:PMC6266932
citation: pubmed:30497367
description: A comparative platform on grapevine and tomato reporting paralog and related ortholog genes identified with an analytical, dedicated, procedure. It provides an update on functional annotations from the two species and it represents an internationally unique platform. It is in expansion in order to include other species, useful to study fruit development.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1

Comorbidity4j
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3063
application sub category: topic 3068
application sub category: topic 3399
citation: btz061
citation: pubmed:30689768
description: Tool for interactive analysis of disease comorbidities over large patient datasets.
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest

CompNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 3372
citation: S12859-019-3168-8
citation: s12859-016-1013-x
citation: pmcid:PMC4845442
citation: pmcid:PMC6869179
citation: pubmed:27112575
citation: pubmed:31747901
description: A GUI based tool for comparison of multiple biological interaction networks. Interaction networks are a convenient way of representing the complex nature of multi-component systems. Examples of such complex systems include biological pathways, social interactions, financial markets, management systems, multiple modules in a programming language, etc. Recognizing the similarities and differences between multiple interaction networks becomes easier when aided by proper visualization tools. we present a GUI based network comparison tool CompNet, which allows to visually compare multiple networks based on node and edge similarities. Additionally, the tool can compare individual networks on the basis of general network properties, node neighborhoods and community similarities. CompNet is expected to be a valuable addition in the field of visual data mining especially for users aiming to visually compare more than two interaction networks at the same time
feature list: operation_0277
feature list: operation 3083

CompScore
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2275
application sub category: topic 3336
citation: ACS.JCIM.9B00343
citation: pubmed:31449403
description: Problems with homepage (January 6th, 2021) | CompScore is a web application for boosting structure-based virtual screening performance by incorporating docking scoring function components into consensus scoring.
feature list: operation_0482
feature list: operation 3501

Compare Two Lists
type: SoftwareApplication
input: ID list
  type: FormalParameter
  additional type: data 2872
  encoding format: format 2330
input: ID list
  type: FormalParameter
  additional type: data 2872
  encoding format: format 2330
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3307
author: https://orcid.org/0000-0001-6358-8380
description: Simple and fast web tool for everyday list comparison, e.g. of genes. Shows the intersection, union, and Jaccard index. Allows easy copying & pasting of comparison results.
feature list: operation 2424
is accessible for free: true

CompleXChange
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic_0749
application sub category: topic 3308
citation: s12859-019-2852-z
citation: pmcid:PMC6547514
citation: pubmed:31159772
description: Differential analysis of combinatorial protein complexes.
feature list: operation 3258
feature list: operation 3630
feature list: operation 3741
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: download

ComplexBrowser
type: SoftwareApplication
input: Expression data
  type: FormalParameter
  additional type: data 2603
  encoding format: format 2330
  encoding format: format 3752
input: Protein interaction data
  type: FormalParameter
  additional type: data_0906
  encoding format: format 3752
output: Protein report
  type: FormalParameter
  additional type: data_0896
  encoding format: format 3752
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 3508
  encoding format: format 3603
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 3508
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0092
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic 2269
application sub category: topic 3520
citation: https://doi.org/10.1101/573774
description: ComplexBrowser is a R based software for supervised analysis of changes in protein complex abundance and subunit co-expression in proteomic datasets. It uses information contained in CORUM and EBI Complex Portal databases to provide the user with visualizations helping with biological interpretation of obtained results. ComplexBrowser also incorporates a normalization and quality control steps.
feature list: operation_0224
feature list: operation_0276
feature list: operation_0531
feature list: operation_0571
feature list: operation 2238
feature list: operation 2428
feature list: operation 2495
feature list: operation 2938
feature list: operation 2939
feature list: operation 2940
feature list: operation 3083
feature list: operation 3282
feature list: operation 3435
feature list: operation 3463
feature list: operation 3659
feature list: operation 3799
operating system: Linux
operating system: Mac
operating system: Windows
software help: Manual.pdf
software version: 1.0

Complex Portal
type: SoftwareApplication
input: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
output: Protein interaction data
  type: FormalParameter
  additional type: data_0906
  encoding format: format 3464
output: Protein interaction data
  type: FormalParameter
  additional type: data_0906
  encoding format: format 3158
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0128
citation: gku975
citation: gky1001
citation: pmcid:PMC4384031
citation: pmcid:PMC6323931
citation: pubmed:25313161
citation: pubmed:30357405
description: The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules. All data is freely available for search and download.
feature list: operation 2422
feature list: operation 3083
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows

CompositeDriver
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0622
application sub category: topic 2640
application sub category: topic 2885
citation: j.cell.2018.02.060
citation: pmcid:PMC6029450
citation: pubmed:29625053
description: CompositeDriver combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
feature list: operation 2454
feature list: operation 3197
feature list: operation 3225
feature list: operation 3504
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software version: 0.2
primary contact: https://orcid.org/0000-0002-3594-6678

ConTEdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0610
application sub category: topic_0780
application sub category: topic_0798
citation: bay131
citation: pmcid:PMC6301336
citation: pubmed:30576494
description: Comprehensive database of transposable elements in conifers.
feature list: operation_0524
feature list: operation 3216
feature list: operation 3431
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
primary contact: Fangqun Ouyang
primary contact: Fei Yi
primary contact: Junhui Wang

Conbase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3168
citation: s13059-019-1673-8
citation: pmcid:PMC6444814
citation: pubmed:30935387
description: Software for unsupervised discovery of clonal somatic mutations in single cells through read phasing.
feature list: operation 3196
feature list: operation 3227
feature list: operation 3454
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Ezeddin Al Hakim
primary contact: Marie Kindblom

ConnectedReads
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0769
application sub category: topic 3168
citation: https://doi.org/10.1101/776807
description: machine-learning optimized long-range genome analysis workflow for next-generation sequencing | a machine-learning optimized long-range genome analysis workflow for next-generation sequencing | Current human genome sequencing assays in both clinical and research settings primarily utilize short-read sequencing and apply resequencing pipelines to detect genetic variants
license: Apache-2.0

Conservation Archive
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0160
application sub category: topic_0610
application sub category: topic 3489
citation: RSTB.2019.0297
citation: pmcid:PMC6863500
citation: pubmed:31679497
description: A database portal containing esources that can be used to infer baseline species conditions.

Conterminator
type: SoftwareApplication
input: NCBI taxonomy ID
  type: FormalParameter
  additional type: data 1179
  encoding format: format 3475
input: NCBI taxonomy ID
  type: FormalParameter
  additional type: data 1179
  encoding format: format 3475
input: Sequence set (nucleic acid)
  type: FormalParameter
  additional type: data 1234
  encoding format: format 1929
input: Sequence set (protein)
  type: FormalParameter
  additional type: data 1233
  encoding format: format 1929
output: Evidence
  type: FormalParameter
  additional type: data 2042
  encoding format: format 3475
output: Evidence
  type: FormalParameter
  additional type: data 2042
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
author: http://orcid.org/0000-0001-8781-9753
citation: https://doi.org/10.1101/2020.01.26.920173
citation: s13059-020-02023-1
citation: pmcid:PMC7218494
citation: pubmed:32398145
description: Conterminator is an efficient method to detect incorrectly labeled sequences across kingdoms by an exhaustive all-against-all sequence comparison. It is free open-source GPLv3-licensed software for Linux and macOS.
feature list: operation 2478
feature list: operation 2479
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: wiki
software version: 1-c74b5
primary contact: http://orcid.org/0000-0001-8781-9753

Context-explorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0108
application sub category: topic_0203
application sub category: topic 2229
citation: journal.pcbi.1006384
citation: pmcid:PMC6331134
citation: pubmed:30601802
description: Analysis of spatially organized protein expression in high-throughput screens.
feature list: operation 3443
feature list: operation 3798
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: context-explorer
primary contact: Joel Ostblom

ContinuousFlex
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic_0102
application sub category: topic_0176
application sub category: topic_0611
citation: pro.3772
citation: j.jsb.2022.107906
citation: pmcid:PMC6933837
citation: pubmed:31693263
citation: pubmed:36244611
description: Hybrid Electron Microscopy Normal Mode Analysis with Scipion. Plugin to use continuousflex protocols within the Scipion framework. This plugin provides HEMNMA and StructMap protocols and is frequently updated.
feature list: operation 2939
feature list: operation 3435
feature list: operation 3457
feature list: operation 3891
license: GPL-3.0

ContraDRG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic 3047
application sub category: topic 3474
citation: FGENE.2019.00990
citation: pmcid:PMC6831742
citation: pubmed:31737032
description: Automatic Partial Charge Prediction by Machine Learning. In recent years, machine learning techniques have been widely used in biomedical research to predict unseen data based on models trained on experimentally derived data. In the current study, we used machine learning algorithms to emulate computationally complex predictions in a reverse engineering-like manner and developed ContraDRG, a software that can be used to predict partial charges for small molecules based on PRODRG and Automated Topology Builder (ATB) predictions. Both tools generate molecular topology files, including the partial atomic charge, by using different procedures.
feature list: operation 2476
feature list: operation 3435
feature list: operation 3893

ConvPath
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0634
application sub category: topic 2229
application sub category: topic 3382
application sub category: topic 3474
citation: J.EBIOM.2019.10.033
citation: pmcid:PMC6921240
citation: pubmed:31767541
description: A software tool for lung adenocarcinoma digital pathological image analysis aided by a convolutional neural network. BACKGROUND:The spatial distributions of different types of cells could reveal a cancer cell's growth pattern, its relationships with the tumor microenvironment and the immune response of the body, all of which represent key "hallmarks of cancer". However, the process by which pathologists manually recognize and localize all the cells in pathology slides is extremely labor intensive and error prone. METHODS:In this study, we developed an automated cell type classification pipeline, ConvPath, which includes nuclei segmentation, convolutional neural network-based tumor cell, stromal cell, and lymphocyte classification, and extraction of tumor microenvironment-related features for lung cancer pathology images.
feature list: operation 3435
feature list: operation 3443
feature list: operation 3659
software help: user manual.php

CorDiff
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0622
application sub category: topic 2269
application sub category: topic 3678
citation: STA4.235
citation: pmcid:PMC6853199
citation: pubmed:31763041
description: Set-based differential covariance testing for genomics. We describe four different summary statistics, to ensure power and flexibility under various settings, including a new connectivity statistic that is sensitive to changes in overall covariance magnitude
feature list: operation 2426
feature list: operation 3435
feature list: operation 3659
license: GPL-2.0

CorEx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3474
citation: https://doi.org/10.3791/60431
citation: pubmed:31657800
description: Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal. Welcome to the CorEx portal for gene expression analysis!. This website began as an extension of work applying the CorEx machine learning algorithm to gene expression data from ovarian cancer tumors as presented in this paper.
feature list: operation 2421
feature list: operation 2495
feature list: operation 3223

CoralTBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3855
citation: S12864-019-5744-8
citation: pmcid:PMC6525400
citation: pubmed:31101011
description: Transcriptomic database for 14 species of scleractinian corals.
feature list: operation 3258
feature list: operation 3431
feature list: operation 3644
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-1541-9627
primary contact: Jianliang Xu

CoreSlicer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3452
citation: s12880-019-0316-6
citation: pmcid:PMC6371488
citation: pubmed:30744586
description: Enables extraction of morphomic markers from CT images by non-technically skilled clinicians.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: video.html
software help: README.md
software help: TERMS.md
primary contact: Louis Mullie

CottonGen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
application sub category: topic_0077
application sub category: topic_0102
application sub category: topic_0622
application sub category: topic_0625
application sub category: topic 3168
citation: BAX092
citation: gkt1064
citation: pmcid:PMC3964939
citation: pmcid:PMC5727400
citation: pubmed:24203703
citation: pubmed:31725859
description: A genomics, genetics and breeding web portal for cotton research.
feature list: operation_0282
feature list: operation 2421
feature list: operation 3196
feature list: operation 3208

CoverageTool
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 3382
citation: S13007-019-0472-2
citation: pmcid:PMC6683572
citation: pubmed:31404403
description: Applications for plant phenotyping | A semiautomated graphic software – applications for plant phenotyping Lianne Merchuk-Ovnat, Ph.D.; Zev Ovnat; Orit Amir-Segev; Yaarit Kutsher; Yehoshua Saranga; Moshe Reuveni Plant Methods | A semiautomated graphic software – applications for plant phenotyping Lianne Merchuk-Ovnat, Ph.D.; Zev Ovnat; Orit Amir-Segev; Yaarit Kutsher; Yehoshua Saranga; Moshe Reuveni Plant Methods 'Coverage.exe' - instructions for use | "o To exclude everything but the interior of a quadrilateral, position cursor over its 4 vertices and click F1, F2, F3 & F4 in clockwise order:" "at top left click F1, at top right click F2, at bottom right click F3, at bottom left click F4." "o Click on radio button 1-10 to select colors to take into account (""Include"") and those to dis-count (""Ignore"")." o Not all 10 + 10 selctions need be filled
feature list: operation 3443
feature list: operation 3799
operating system: Windows

CowpeaMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: A mine containing both cowpea genetic and genomic data, courtesy UC-Riverside
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 0.10

Cox-PASNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3379
application sub category: topic 3474
citation: S12920-019-0624-2
citation: pmcid:PMC6927105
citation: pubmed:31865908
description: Interpretable deep neural network for cancer survival analysis by integrating genomic and clinical data. Pathway-based sparse deep neural network for survival analysis. Cox-PASNet is a pathway-based sparse deep neural network for survival analysis
feature list: operation 2428
feature list: operation 2495
feature list: operation 2497

CpGtools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3518
application sub category: topic 3674
citation: btz916
citation: pmcid:PMC8275978
citation: pubmed:31808791
description: A Python Package for DNA Methylation Analysis. Python package to analyze DNA methylation data. $ pip3 install git+https://github.com/liguowang/cpgtools.git
feature list: operation 3204
feature list: operation 3659
feature list: operation 3891
license: GPL-3.0

CpnClassiPhyR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0780
application sub category: topic 2885
application sub category: topic 3293
citation: PDIS-03-19-0454-A
citation: pubmed:31453748
description: The CpnClassiPhyR Is a Resource for cpn60 Universal Target-Based Classification of Phytoplasmas | Welcome to the CpnClassiPhyR Github Page! | a cpn60 universal target-based classification tool for phytoplasma | Phytoplasmas (‘Candidatus Phytoplasma’), first known as mycoplasma-like organisms, are wall-less, insect vectored bacteria that cause disease in more than a thousand different plant hosts, affecting weedy, ornamental and crop plants worldwide | Following the strategy previously used in the phytoplasma classification scheme based on the 16S rRNA gene, we developed a complementary, coherent system to classify phytoplasmas based on RFLP analysis of cpn60 UT sequences with seven endonucleases
feature list: operation 3192
feature list: operation 3460
feature list: operation 3891

Cram-JS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3673
application sub category: topic 3676
citation: btz384
citation: pmcid:PMC6821367
citation: pubmed:31099383
description: Reference-Based Decompression in Node and the Browser.
feature list: operation_0337
feature list: operation 2422
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Robert Buels

Crisflash
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
citation: btz019
citation: pmcid:PMC6735888
citation: pubmed:30649181
description: Software to generate CRISPR guide RNAs against genomes annotated with individual variation.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Margus Lukk

CropCircDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3512
citation: BAZ053
citation: pmcid:PMC6501434
citation: pubmed:31058278
description: Comprehensive circular RNA resource for crops in response to abiotic stress.
feature list: operation 3431
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Tutorial
primary contact: https://orcid.org/0000-0002-2425-3526
primary contact: Hongwei Zhao

Cropper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0625
application sub category: topic 3517
citation: s12859-019-2600-4
citation: pmcid:PMC6330393
citation: pubmed:30634901
description: GUI application for viewing and handling Manhattan Plots. The user can zoom, select and crop Manhattan Plots and generate output both in the graphical and numerical format.
feature list: operation 3222
feature list: operation 3557
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: T. Haller

Crossmapper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3174
application sub category: topic 3308
author: Ahmed Hafez
author: Hrant Hovhannisyan
citation: btz626
citation: pmcid:PMC7049214
citation: pubmed:31392323
description: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies | General descripiton of Crossmapper | Crossmapper is an automated bioinformatics pipeline for asessing the rate of read crossmapping when two or more organisms are sequenced as one sample. The software can be used for planning such kind of experimental setups as dual- or multiple RNA-seq (mainly for host-pathogen, symbiont and cohabitant interaction studies), metagenomics studies, sequencing and analysis of hybrid species, allele-specific expression studies, and can be extended for the use in large sequencing facilities for resource optimization
license: GPL-3.0
software help: wiki
software version: v1.1.1

CrowdGO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0610
citation: https://doi.org/10.1101/731596
description: A wisdom of the crowd-based Gene Ontology annotation tool | Abstract Motivation Protein function prediction tools vary widely in their methodologies, resulting in different sets of GO terms being correctly predicted. Ideally, multiple tools are combined to achieve a higher recall of GO terms while increasing precision. Results CrowdGO combines input predictions from any number of tools and combines them based on the Gene Ontology Directed Acyclic Graph. Using each GO terms information content, the semantic similarity between GO predictions of different tools, and a Support Vector Machine model, it achieves improved precision and recall compared to each of the tools separately (Figure 1). Availability CrowdGO can be found at https: gitlab.com mreijnders CrowdGO
license: GPL-3.0

Crowdbreaks
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0218
application sub category: topic 3305
application sub category: topic 3474
citation: FPUBH.2019.00081
citation: pmcid:PMC6476276
citation: pubmed:31037238
description: Tracking Health Trends Using Public Social Media Data and Crowdsourcing.
feature list: operation_0560
feature list: operation 3501
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
primary contact: Marcel Salathé
primary contact: Martin Müller

Cryfa
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3263
citation: bty645
citation: pmcid:PMC6298042
citation: pubmed:30020420
description: Secure encryption tool for genomic data, namely in Fasta, Fastq, VCF, SAM and BAM formats, which is also capable of reducing the storage size of Fasta and Fastq files.
feature list: operation 3436
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Morteza Hosseini

CryoFLARE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3077
application sub category: topic 3382
citation: acs.jcim.9b01102
citation: https://doi.org/10.1101/861740
citation: pubmed:32233514
description: Live analysis and reconstruction of single-particle cryo-electron microscopy data with CryoFLARE. CryoFLARE: FMI Live Analysis and Reconstruction Engine for single particle Cryo EM data. The FMI Live Analysis and Reconstruction Engine. Live analysis of Cryo EM data made easy. Import data from EPU or SerialEM
feature list: operation 2422
feature list: operation 2940
feature list: operation 3457
software help: documentation
software help: cryoflare-scripting-bridge

CrystFEL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0611
application sub category: topic 2828
application sub category: topic 3452
citation: S0021889812002312
citation: S205979831801238X
citation: pmcid:PMC6400257
citation: pubmed:30821710
description: Software for processing serial crystallography data from an X-ray free-electron laser or a synchrotron light source.
feature list: operation_0337
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: faq.html
software help: install.html
software help: manual.html
software help: tutorial.html
primary contact: Thomas White

CrystaLattE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3314
application sub category: topic 3474
citation: https://doi.org/10.1063/1.5120520
citation: pubmed:31615262
description: Automated computation of lattice energies of organic crystals exploiting the many-body expansion to achieve dual-level parallelism. Set of scripts to automate the calculation of crystal lattice energies. Automated calculation of crystal lattice energies with the many-body expansion. CrystaLattE has an interface with the quantum chemistry package PSI4. To run, the code requires a crystallographic information file containing structural information of the crystal and an input file specifying execution details. Work continues in the creation of a CrystaLattE pip package. So, for the moment, the instructions to download and install CrystaLattE and to create a conda environment that includes PSI4 are presented below. CyrstaLattE is a software that automates the computation of crystal lattice energies using the many-body cluster expansion
feature list: operation 3432
license: LGPL-3.0

Cumulus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0769
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3416
citation: https://doi.org/10.1101/823682
description: A cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seq. Cumulus WDL workflows and Dockerfiles. Interactive single cell visualization in the cloud or on your desktop. Cumulus WDL workflows and Dockerfiles — Cumulus documentation. Clone the cirrocumulus repository:. Google Cloud Platform (GCP) Deployment Instructions. Free document hosting provided by Read the Docs
feature list: operation 2939
feature list: operation 3096
feature list: operation 3680
license: BSD-3-Clause
software help: stable

Curatopes Melanoma
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0804
application sub category: topic 3379
application sub category: topic 3400
citation: 0008-5472.CAN-19-0296
citation: pubmed:31416842
description: A Database of Predicted T-cell Epitopes from Overly Expressed Proteins in Metastatic Cutaneous Melanoma | Browse and download predicted melanoma epitopes with high expected clinical efficacy in anti-cancer immunotherapy | This page acts as a gateway to the Curatopes Melanoma database
feature list: operation_0416
software help: documentation.html

CutpointsOEHR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3305
application sub category: topic 3315
citation: S12874-019-0738-4
citation: pmcid:PMC6507062
citation: pubmed:31072334
description: Optimal Equal-HR Method to Find Two Cutpoints for U-Shaped Relationships in Cox Model.
feature list: operation_0490
feature list: operation 3659
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: CutpointsOEHR.pdf
primary contact: https://orcid.org/0000-0002-1123-5556

CyGenexpi
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3751
output: Pathway or network report
  type: FormalParameter
  additional type: data 2984
  encoding format: format 3751
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic_0204
author: http://orcid.org/0000-0002-8886-7797
citation: s12859-018-2138-x
citation: pmcid:PMC5899412
citation: pubmed:29653518
description: CyGenexpi is a Cytoscape plugin for validating/inferring genetic networks from time series expression data. It is based on a ordinary differential equation (ODE) model of gene regulation.
feature list: operation 1781
funder: Ministry of Education, Youth and Sports of the Czech Republic
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: CyGenexpi
software version: 1.3.0
software version: 1.4.2
primary contact: http://orcid.org/0000-0002-8886-7797

CyTOF workflow
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic 3360
citation: F1000RESEARCH.11622.3
citation: pmcid:PMC5473464
citation: pubmed:28663787
description: Differential discovery in high-throughput high-dimensional cytometry datasets.
feature list: operation 2938
feature list: operation 2939
feature list: operation 3436
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: cytofWorkflow
primary contact: https://orcid.org/0000-0002-3048-5518

CyTargetLinker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic 3474
citation: F1000RESEARCH.14613.2
citation: journal.pone.0082160
citation: pmcid:PMC3855388
citation: pmcid:PMC6707396
citation: pubmed:24340000
citation: pubmed:31489175
description: A flexible solution for network extension in Cytoscape | The CyTargetLinker app extends biological networks with regulatory interactions, for example miRNA-target, TF-target or drug-target interactions | CyTargetLinker website and tutorials | CyTargetLinker - Extend your biological networks in Cytoscape
feature list: operation_0277
feature list: operation 1781
feature list: operation 3439
software help: citation
software help: docs

CycloNovo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3520
application sub category: topic 3697
citation: J.CELS.2019.11.007
citation: pubmed:31864964
description: De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. CycloNovo: Algorithm for de novo cyclopeptide analysis of high-resolution tandem mass spectra. CycloNovo is a new algorithm that identifies spectra generated from cyclopeptides in large mass spectrometry datasets. CycloNovo can also de novo sequence the cyclopeptides represented by identified cyclospectra
feature list: operation_0524
feature list: operation 3644
feature list: operation 3860

Cyclum
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2229
application sub category: topic 2269
application sub category: topic 3170
citation: https://doi.org/10.1101/625566
description: Package to tackle cell cycle. It provides methods to recover cell cycle information and remove cell cycle factor from the scRNA-seq data.
feature list: operation 2436
feature list: operation 3629
feature list: operation 3891
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

CytoConverter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0654
application sub category: topic 3168
application sub category: topic 3518
citation: S12859-019-3062-4
citation: pmcid:PMC6739950
citation: pubmed:31510921
description: A web-based tool to convert karyotypes to genomic coordinates | Sequence-Cytogenetic Bulk Conversion | Bulk Sequence - Cytogenetic Conversion Service | Use this page to get cytogenetic locations for features or sequence locations, or get sequence locations for cytogenetic locations | Organism: Drosophila melanogaster Homo sapiens Mus musculus Rattus norvegicus
feature list: operation 1812
feature list: operation 3196

CytoGPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web application
application sub category: topic_0654
application sub category: topic 3303
application sub category: topic 3518
citation: btab683
citation: btz520
description: CytoGenetic Pattern Sleuth (CytoGPS) - web-enabled karyotype analysis tool for cytogenetics.
feature list: operation 1812
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.8
primary contact: Institute for Informatics, Washington University School of Medicine

CytoNorm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3934
citation: CYTO.A.23904
citation: pmcid:PMC7078957
citation: pubmed:31633883
description: A Normalization Algorithm for Cytometry Data. A R library to normalize cytometry data.
feature list: operation 3200
feature list: operation 3432
feature list: operation 3435
feature list: operation 3436
license: GPL-2.0
software help: man
software version: 0.0.5

CytoPacq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2229
application sub category: topic 3382
citation: btz417
citation: pmcid:PMC6821329
citation: pubmed:31114843
description: Web-interface for simulating multi-dimensional cell imaging.
feature list: operation 3629
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: cytopacq.html

CytoTRACE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2229
application sub category: topic 3308
application sub category: topic 3395
citation: https://doi.org/10.1101/649848
description: Single-cell transcriptional diversity is a hallmark of developmental potential
feature list: operation 2436
feature list: operation 3799
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: shiny-tab-FAQ
software help: shiny-tab-Tutorials

Cytokit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic 2830
application sub category: topic 3360
application sub category: topic 3382
citation: S12859-019-3055-3
citation: pmcid:PMC6720861
citation: pubmed:31477013
description: A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging | Microscopy Image Cytometry Toolkit | Cytokit is a collection of tools for quantifying and analyzing properties of individual cells in large fluorescent microscopy datasets with a focus on those generated from multiplexed staining protocols. This includes a GPU-accelerated image processing pipeline (via TensorFlow), CLI tools for batch processing of experimental replicates (often requiring conditional configuration, as things tend go wrong when capturing hundreds of thousands of microscope images over a period of hours or days), and visualization UIs (either Cytokit Explorer or CellProfiler Analyst) | Med Google Cloud Platform kan du oprette, implementere og skalere apps, websites og tjenester på den samme infrastruktur som Google | Fortsæt til Google Cloud Platform | Skriv den tekst, du hører eller ser
feature list: operation 3552
feature list: operation 3629
license: Apache-2.0

Cytomine
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0634
application sub category: topic 3382
citation: prca.201800057
citation: pubmed:30520559
description: Tool for collaborative multimodal imaging and our latest software developments to support next-generation digital pathology bridged to molecular investigations.
feature list: operation_0337
feature list: operation 3799
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: doc.cytomine.be

Cytoscape Automation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Suite
additional type: Workflow
application sub category: topic_0602
application sub category: topic_0769
application sub category: topic 3293
citation: S13059-019-1758-4
citation: pmcid:PMC6717989
citation: pubmed:31477170
description: Cytoscape Automation combines Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio.
feature list: operation 2497
feature list: operation 3501
is accessible for free: true
license: CC0-1.0

D-lnc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic_0659
citation: https://doi.org/10.1080/15476286.2019.1649584
citation: pmcid:PMC6779407
citation: pubmed:31390943
description: A comprehensive database and analytical platform to dissect the modification of drugs on lncRNA expression
feature list: operation 2495
feature list: operation 3223

D3E
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3475
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic 3308
citation: s12859-016-0944-6
citation: pmcid:PMC4772470
citation: pubmed:26927822
description: Identification of differentially-expressed genes in single-cell RNA sequencing data.
feature list: operation 3223
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Example
software help: User-Guide

D3GRN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 2259
application sub category: topic 3474
application sub category: topic 3518
citation: S12864-019-6298-5
citation: pmcid:PMC6933629
citation: pubmed:31881937
description: a data driven dynamic network construction method to infer gene regulatory networks. Gene regulatory network;Dynamic networks construction;Regression;DREAM challenge. D3GRN is a Data Driven Dynamic network construction method to infer Gene Regulatory Networks
feature list: operation 1781
feature list: operation 3439
feature list: operation 3659
license: MIT

DAMEfinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0749
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3295
application sub category: topic 3674
citation: https://doi.org/10.1101/800383
citation: s13072-020-00346-8
citation: pmcid:PMC7268773
citation: pubmed:32487212
description: DAMEfinder (Differential Allele-specific MEthylation finder) is an R-package that detects allele-specific methylation (ASM) in a cohort of samples, and detects regions of differential ASM within groups of interest, based on Bisulfite-sequencing files.
feature list: operation 3186
feature list: operation 3196
feature list: operation 3207

DAMIAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic 3168
application sub category: topic 3301
application sub category: topic 3324
application sub category: topic 3388
citation: S41598-019-52881-4
citation: pmcid:PMC6856179
citation: pubmed:31727957
description: An open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples. Identification of pathogenic microorganisms in diagnostic samples. DAMIAN provides capabilities to detect known and novel pathogens in RNA and DNA samples of various sources. It integrates all required processing steps, ranging from the quality control of sequencing reads to the generation of comprehensive reports. The method works for any host organism
feature list: operation 3196
feature list: operation 3218
feature list: operation 3460
feature list: operation 3461
license: GPL-3.0

DAStk - Differential ATAC-seq toolkit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
citation: molecules23051136
citation: pmcid:PMC6099720
citation: pubmed:29748466
contributor: https://orcid.org/0000-0001-5808-5308
description: The Differential ATAC-seq Toolkit (DAStk) is a set of command-line tools to aid analyzing differential ATAC-seq data. By leveraging changes in accessible chromatin, we can detect significant changes in transcription factor (TF) activity. This is a simple but powerful tool for cellular perturbation analysis. In fact, the applications of DAStk are not necessarily limited to ATAC-seq, but can extend to comparing any pair of bedGraphs containing regions of interest, e.g. transcription regulatory elements (TRE) from nascent transcription assays like PRO-seq, or others like ChIP-seq peaks. To aid downstream analysis, DAStk also includes a graph that combines all human proteins in Uniprot, with their respective annotations, and all human Reactome data on biological pathways, biochemical reactions, and complex formation. This allows the user to query for existing knowledge about what aspects of the significantly changing TFs are shared among two or more of them.
feature list: operation 2437
feature list: operation 3677
feature list: operation 3741
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
software version: 1.0.0
primary contact: https://orcid.org/0000-0003-3066-4273

DBH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3384
application sub category: topic 3474
application sub category: topic 3810
citation: PREPRINTS201907.0158.V1
description: > HOMEPAGE MISSING! | > CORRECT NAME OF TOOL COULD ALSO BE 'hyperspectral', 'vegetation', 'planation', 'Cunninghamia' | UAV-Based High-Throughput Approach for Fast Growing Cunninghamia lanceolata (Lamb.) Cultivar Screening by Machine Learning | Accurate measurements of tree height and diameter at breast height (DBH) in forests to evaluate the growth rate of cultivars is still a significant challenge, even when using LiDAR and 3-D modeling. We propose an integrated pipeline methodology to measure the biomass of different tree cultivars in plantation forests with high crown density which that combines unmanned aerial vehicles (UAVs), hyperspectral image sensors, and data processing algorithms using machine learning. Using a planation of Cunninghamia lanceolate, commonly known as Chinese fir, in Fujian, China, images were collected using a hyperspectral camera and orthorectified in HiSpectral Stitcher

DBTL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic 3474
application sub category: topic 3895
citation: ACSSYNBIO.9B00020
citation: pubmed:31072100
description: The Design Build Test Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts in biofuels and bio-based products.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Harry R. Beller

DCA
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3475
output: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2269
application sub category: topic 3308
citation: s41467-018-07931-2
citation: pmcid:PMC6344535
citation: pubmed:30674886
description: Deep count autoencoder for denoising scRNA-seq data.
feature list: operation 3557
feature list: operation 3664
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial.ipynb

DCMF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0084
application sub category: topic_0780
application sub category: topic 3673
citation: PEERJ.PREPRINTS.27718
description: Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture.
feature list: operation_0552
feature list: operation_0558
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: R. J. Edwards

DDAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 2275
citation: https://doi.org/10.1101/637405
description: Docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases.
feature list: operation_0436
feature list: operation 3439
feature list: operation 3803
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

DDI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0202
application sub category: topic_0602
application sub category: topic 3375
citation: 1062936X.2019.1653966
citation: pubmed:31482727
description: Drug-drug interaction prediction using PASS | DDI-Pred: web-service for drug-drug interaction prediction
feature list: operation_0272
feature list: operation 2492
feature list: operation 3901

Data dependent-independent acquisition proteomics (DDIA)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: https://doi.org/10.1101/802231
description: Data dependent-independent acquisition proteomics (DDIA) is a pipeline for combining and analysing Data dependent acquisition (DDA) and data independent acquisition (DIA) proteomics data.
feature list: operation 3436
feature list: operation 3631
feature list: operation 3767

DDPGPSurv
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3375
application sub category: topic 3399
application sub category: topic 3421
citation: RSSC.12331
citation: pmcid:PMC6714050
citation: pubmed:31467455
description: Bayesian non-parametric survival regression for optimizing precision dosing of intravenous busulfan in allogeneic stem cell transplantation | Allogeneic stem cell transplantation (allo-SCT) is now part of standard of care for acute leukemia (AL). To reduce toxicity of the pre-transplant conditioning regimen, intravenous busulfan is usually used as a preparative regimen for AL patients undergoing allo-SCT. Systemic busulfan exposure, characterized by the area under the plasma concentration versus time curve (AUC), is strongly associated with clinical outcome. An AUC that is too high is associated with severe toxicities, while an AUC that is too low carries increased risks of disease recurrence and failure to engraft. Consequently, an optimal AUC interval needs to be determined for therapeutic use
feature list: operation 3659

DDR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3360
application sub category: topic 3518
citation: S12859-019-3140-7
citation: pmcid:PMC6868758
citation: pubmed:31752658
description: Multiplatform biomarker identification using a data-driven approach enables single-sample classification.
feature list: operation 2495
feature list: operation 3223
feature list: operation 3435

DDT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0176
application sub category: topic 2275
application sub category: topic 3336
citation: btz543
description: DDT (Drug Discovery Tool) - graphics user interface for Docking and Molecular Dynamics analysis
feature list: operation_0482
feature list: operation 2476
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://www.youtube.com/watch
primary contact: Vittorio Limongelli

DDVFA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3382
application sub category: topic 3474
citation: J.NEUNET.2019.08.033
citation: pubmed:31574412
description: Distributed dual vigilance fuzzy adaptive resonance theory learns online, retrieves arbitrarily-shaped clusters, and mitigates order dependence. Dual Vigilance Fuzzy ART - Companion MATLAB Code. Distributed Dual Vigilance Fuzzy ART - Companion MATLAB Code.
feature list: operation 2422
feature list: operation 3432
feature list: operation 3891
license: Apache-2.0

DECIPHER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic 3325
application sub category: topic 3404
citation: humu.22842
citation: V1
citation: pmcid:PMC4832335
citation: pubmed:26220709
description: Web-based platform for secure deposition, analysis, and sharing of plausibly pathogenic genomic variants from well-phenotyped patients suffering from genetic disorders.
feature list: operation 3196
feature list: operation 3226
feature list: operation 3431
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software version: 9.29
primary contact: Ganesh Swaminathan

DEEPCON
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3474
citation: BTZ593
citation: pubmed:31359036
description: Protein Contact Prediction using Dilated Convolutional Neural Networks with Dropout
feature list: operation_0272
feature list: operation 3439

DEEPSEN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0199
application sub category: topic_0749
application sub category: topic 3474
citation: S12859-019-3180-Z
citation: pmcid:PMC6929276
citation: pubmed:31874597
description: A convolutional neural network based method for super-enhancer prediction. data and material In this folder, we include all the material and data used in the DEEPSEN
feature list: operation_0331
feature list: operation 3439

DEEPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic 3474
citation: S41598-019-43708-3
citation: pmcid:PMC6517386
citation: pubmed:31089211
description: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks.
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ReadMe.md
primary contact: Tunca Doğan
primary contact: Volkan Atalay

DEN-IM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3174
application sub category: topic 3293
application sub category: topic 3837
citation: https://doi.org/10.1101/628073
description: Dengue Virus identification from shotgun and targeted metagenomics.
feature list: operation_0310
feature list: operation 2495
feature list: operation 3196
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Bioinformatics, Molecular Microbiology and Infection Unit

DENOPTIM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic 2258
application sub category: topic 3332
application sub category: topic 3343
application sub category: topic 3474
citation: ACS.JCIM.9B00516
citation: pubmed:31479254
description: Software for Computational de Novo Design of Organic and Inorganic Molecules | DENOPTIM is a software package for de novo design and virtual screening of functional molecules of any kind | DENOPTIM (De Novo OPTimization of In/organic Molecules) is a software meant for de novo design and virtual screening of functional compounds. In practice, DENOPTIM is meant for building chemical entities by assembling building blocks (i.e., fragments), processing each chemical entity as to produce its figure of merit (i.e., fitness), and designing new entities based on the properties of entities generated before.
feature list: operation_0476
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: http://htmlpreview.github.io/

DENSIFE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3344
application sub category: topic 3382
description: Densitometry software written for Mathlab.
feature list: operation 3552
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: Lorena

DEOGEN2
type: SoftwareApplication
input: UniProt accession
  type: FormalParameter
  additional type: data 3021
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
author: Daniele Raimondi
author: Ibrahim Tanyalcin
citation: gkx390
citation: pmcid:PMC5570203
citation: pubmed:28498993
description: Sequence-based predictor of deleteriousness of amino acid variants in human proteins
feature list: operation_0331
primary contact: https://orcid.org/0000-0001-7470-4324

DEPIB
type: SoftwareApplication
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1931
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2331
output: Clustered expression profiles
  type: FormalParameter
  additional type: data 3768
  encoding format: format 3508
  encoding format: format 3603
output: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3751
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic 3308
author: https://orcid.org/0000-0002-8689-2083
author: https://orcid.org/0000-0003-3237-7382
author: Eric Charpentier
author: Erwan Delage
citation: stem.3014
citation: s41419-019-2200-2
citation: pmcid:PMC6850038
citation: pmcid:PMC6944699
citation: pubmed:30977188
citation: pubmed:31907355
contributor: Damien Vintache
description: Analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes.
feature list: operation 3800
is accessible for free: true
provider: BiRD bioinformatics facility
software version: 1.0
primary contact: Eric Charpentier

DEPICTER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic 3334
application sub category: topic 3538
citation: J.JMB.2019.12.030
citation: pubmed:31870849
description: Intrinsic disorder and disorder function prediction server. Predictors of disordered regions and their molecular functions - web server from Biomine lab. DEPICTER : DisorderEd PredictIon CenTER
feature list: operation_0470
feature list: operation 1777
feature list: operation 1812
feature list: operation 3904

Human Dephosphorylation Database (DEPOD)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic_0160
application sub category: topic_0219
application sub category: topic 3489
citation: BAZ133
citation: pmcid:PMC6911163
citation: pubmed:31836896
description: DEPOD - the human DEPhOsphorylation Database, is a manually curated database collecting human phosphatases, their experimentally verified substrates and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates.
feature list: operation_0417
feature list: operation 3083
feature list: operation 3208

DEPOT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3322
application sub category: topic 3384
application sub category: topic 3452
citation: JOURNAL.PONE.0217410
citation: pmcid:PMC6532897
citation: pubmed:31120982
description: Multi-domain tuberculosis data analysis resource.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Andrei Gabrielian

Deep Sequence and Shape Motif (DESSO)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Database portal
additional type: Web application
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3510
citation: GKZ672
citation: pmcid:PMC6735894
citation: pubmed:31372637
description: DESSO is a deep learning-based framework that can be used to accurately identify both sequence and shape regulatory motifs from the human genome.
feature list: operation_0238
feature list: operation_0441
feature list: operation_0445

DEUS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0659
application sub category: topic 3170
author: Maximilian Hastreiter
author: Tim Jeske
citation: btz495
citation: pmcid:PMC6853685
citation: pubmed:31228198
description: R package for accurate small RNA profiling based on differential expression of unique sequences.
feature list: operation 2495
feature list: operation 3198
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: DEUS.html
software help: SampleUsage.html
primary contact: Tim Jeske

DEWE: Differential Expression Workflow Executor
type: SoftwareApplication
input: RNA sequence (raw)
  type: FormalParameter
  additional type: data 3496
  encoding format: format 1930
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0080
citation: j.compbiomed.2019.02.021
citation: pubmed:30849608
description: DEWE is a software tool to perform genetic differential expression analysis of RNA-Seq data. DEWE offers built-in, easy-to-configure workflows that facilitate the execution of DE analyses. Currently, DEWE provides two differential expression analysis workflows: HISAT2, StringTie and R libraries (Ballgown and edgeR) and Bowtie2, StringTie and R libraries (Ballgown and edgeR).
feature list: operation 3223
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: manual.html
software version: 1.2.0

DEvis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
application sub category: topic 3308
citation: s12859-019-2702-z
citation: pmcid:PMC6399874
citation: pubmed:30832568
description: R package for aggregation and visualization of differential expression data.
feature list: operation 2495
feature list: operation 3436
feature list: operation 3741
is accessible for free: true
license: LGPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: DEvis
primary contact: Adam Price

DIA-DB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0780
application sub category: topic 3407
citation: ACS.JCIM.0C00107
citation: MOLECULES24102002
citation: pmcid:PMC6571761
citation: pubmed:31137754
citation: pubmed:32692571
description: DIA-DB is a web server for the prediction of diabetes drugs that uses two different approaches; a) comparison by similarity with a curated database of anti-diabetic drugs and experimental compounds, and b) inverse virtual screening of the input molecules chosen by the users against a set of protein targets identified as key elements in diabetes.
feature list: operation_0394
feature list: operation_0482
feature list: operation 3216
is accessible for free: true
license: CC-BY-NC-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: FAQ.php
software help: Tutorial.php
primary contact: https://orcid.org/0000-0003-4468-7898
primary contact: Zeno Apostolides

DIA-NN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
additional type: Library
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3474
application sub category: topic 3520
citation: s41592-019-0638-x
citation: pmcid:PMC6949130
citation: pubmed:31768060
description: Neural networks and interference correction enable deep proteome coverage in high throughput. DIA-NN - a fast and easy to use tool for processing data independent acquisition (DIA) proteomics data. None required (for .raw, .mzML and .dia processing). Two executables are provided: DiaNN.exe (a command-line tool) and DIA-NN.exe (a GUI implemented as a wrapper for DiaNN.exe)
feature list: operation 3767
feature list: operation 3799
feature list: operation 3801
software help: DIA-NN GUI manual.pdf

DIA-Umpire
type: SoftwareApplication
input: Mass spectrometry spectra
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3651
  encoding format: format 3654
input: Sequence set
  type: FormalParameter
  additional type: data_0850
  encoding format: format 1929
input: Expression data
  type: FormalParameter
  additional type: data 2603
  encoding format: format 3655
  encoding format: format 3747
input: Mass spectrometry spectra
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3654
output: Mass spectrometry spectra
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3651
output: Expression data
  type: FormalParameter
  additional type: data 2603
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic 3520
citation: nmeth.3255
citation: pmcid:PMC4399776
citation: pubmed:25599550
description: DIA-Umpire is an open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. It enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation.
feature list: operation 3215
feature list: operation 3627
feature list: operation 3630
feature list: operation 3631
feature list: operation 3633
feature list: operation 3649
feature list: operation 3801
feature list: operation 3860
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Manual
software version: 2.0
primary contact: Chih-Chiang Tsou

Debris Identification using Expectation Maximization (DIEM)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3474
application sub category: topic 3512
citation: s41598-020-67513-5
citation: https://doi.org/10.1101/786285
citation: pmcid:PMC7335186
citation: pubmed:32620816
description: Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM. Remove debris-contaminated droplets from single-cell based data
feature list: operation_0313
feature list: operation 2238
feature list: operation 3192

DIFFUSE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3320
application sub category: topic 3474
application sub category: topic 3512
citation: BTZ367
citation: pmcid:PMC6612874
citation: pubmed:31510699
description: predicting isoform functions from sequences and expression profiles via deep learning | Deep learning based prediction of IsoForm FUnctions from Sequences and Expression | DIFFUSE is a deep learning based method for predicting isoform functions by integrating the data of isoform sequences, domains and expression profiles.
feature list: operation_0264
feature list: operation 3766
feature list: operation 3798
license: MIT

Disease-gene Immune cell Expression (DIME)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic_0804
application sub category: topic 3308
citation: https://doi.org/10.1101/2019.12.12.874321
description: Integration of immunome with disease gene network reveals pleiotropy and novel drug repurposing targets. Abstract Immune system is crucial for the development and progression of immune-mediated and non-immune mediated complex diseases. Studies have shown that multiple complex diseases are associated with several immunologically relevant genes. Despite such growing evidence, the effect of disease associated genes on immune functions has not been well explored. Here, we curated the largest immunome (transcriptome profiles of 40 different immune cells) and integrated it with disease gene networks and drug-gene database, to generate a Disease-gene IMmune cell Expression network (DIME). Is a Shiny app.
feature list: operation 2495

DIMERBOW
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0153
application sub category: topic_0202
application sub category: topic_0820
application sub category: topic 3300
application sub category: topic 3892
citation: btaa117
citation: https://doi.org/10.1101/836213
citation: pubmed:32096817
description: Exploring and visualizing possible GPCR dimer.
feature list: operation_0269
feature list: operation_0337
feature list: operation 2995
software help: manual

Diffusion Imaging in Python (DIPY)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Suite
application sub category: topic 3384
application sub category: topic 3444
citation: fninf.2014.00008
citation: pmcid:PMC3931231
citation: pubmed:24600385
description: DIPY is a free and open source software project for the analysis of data from diffusion magnetic resonance imaging (dMRI) experiments
feature list: operation 2939
feature list: operation 3446
feature list: operation 3891

Direct Information Reweighted by Contact Templates (DIRECT)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0099
citation: S12859-019-3099-4
citation: pmcid:PMC6794908
citation: pubmed:31615418
description: RNA contact predictions by integrating structural patterns. It is widely believed that tertiary nucleotide-nucleotide interactions are essential in determining RNA structure and function.
feature list: operation_0267
feature list: operation_0272
feature list: operation_0278
feature list: operation_0474
feature list: operation 2441

Design of an Identifiable Synthetic Community of Microbes (DISCo-microbe)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0780
application sub category: topic 3174
application sub category: topic 3697
citation: PEERJ.PREPRINTS.27898V1
description: DISCo-microbe is an easy-to-use command-line program, for creation of diverse communities of organisms that can be distinguished through next-generation sequencing technology
feature list: operation 3192
feature list: operation 3460
license: GPL-3.0

DISNOR
type: SoftwareApplication
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 3242
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
  encoding format: format 3242
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0602
application sub category: topic 3325
author: Alberto Calderone
author: Prisca Lo Surdo
citation: pubmed:29036667
contributor: Gianni Cesareni
contributor: Luana Licata
contributor: Marta Iannuccelli
description: A disease-focused resource that uses the causal interaction information annotated in SIGNOR and the protein interaction data in mentha to generate and explore protein interaction networks linking disease genes.
feature list: operation 3083
feature list: operation 3431
is accessible for free: true
license: CC-BY-NC-4.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: Molecular Genetic Group, University of Rome "Tor Vergata", Rome, Italy
software help: disnor.uniroma2.it
primary contact: Livia Perfetto

DISOselect
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0108
application sub category: topic_0123
application sub category: topic 3538
citation: PRO.3756
citation: pmcid:PMC6933862
citation: pubmed:31642118
description: Disorder predictor selection at the protein level. DISOselect accepts either single or multiple protein sequences. The input is limited to 1000 protein sequences. The user should submit the protein sequence(s) in FASTA format
feature list: operation_0468
feature list: operation_0470
feature list: operation 3904

Distribution-based modeling of Sequence space time dynamics (DISSEQT)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3168
application sub category: topic 3569
citation: VEZ028
citation: pmcid:PMC6680062
citation: pubmed:31392032
description: The complete analysis of deep sequencing data from the DISSEQT paper is available at the collaborative science platform Synapse here. In order to view and download files you must create a Synapse account. (The scripts are also available in the examples folder for reference, but note that you will need a Synapse account to access the data files.)
feature list: operation_0487
feature list: operation 2939
feature list: operation 3196
license: MIT

DIpartite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3169
citation: JOURNAL.PONE.0220207
citation: pmcid:PMC6716629
citation: pubmed:31469855
description: A tool for detecting bipartite motifs by considering base interdependencies | A DNA sequence motif finding program | DIpartite is a tool for detecting bipartite motif based on dinucleotide weight matrix | DIpartite predicts transcription factor binding sites (TFBSs) based on PWM or DWM. Bipartite motif is defined as two conserved blocks separated by variable gaps
feature list: operation_0239
feature list: operation_0445
feature list: operation_0476
license: GPL-3.0

DL-SDM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3050
application sub category: topic 3474
citation: https://doi.org/10.1101/744441
description: Modelling the niches of wild and domesticated Ungulate species using deep learning | Abstract Knowledge of global biodiversity remains limited by geographic and taxonomic sampling biases. The scarcity of species data restricts our understanding of the underlying environmental factors shaping distributions, and the ability to draw comparisons among species. Species distribution models (SDMs) were developed in the early 2000s to address this issue. Although SDMs based on single layered Neural Networks have been experimented with in the past, these performed poorly. However, the past two decades have seen a strong increase in the use of Deep Learning (DL) approaches, such as Deep Neural Networks (DNNs). Despite the large improvement in predictive capacity DNNs provide over shallow networks, to our knowledge these have not yet been applied to SDM
license: MIT

DLIGAND2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic 2275
citation: S13321-019-0373-4
citation: pmcid:PMC6686496
citation: pubmed:31392430
description: An improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state | DLIGAND2 is a knowledge-based method to predict protein-ligand binding affinity based on a distance-scaled, finite, ideal-gas reference (DFIRE) state
feature list: operation_0482
feature list: operation 3501
feature list: operation 3899
license: MIT

DLITE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2229
citation: J.BPJ.2019.09.034
citation: pmcid:PMC6838938
citation: pubmed:31648791
description: DLITE Uses Cell-Cell Interface Movement to Better Infer Cell-Cell Tensions. Cell shapes and connectivities evolve over time as the colony changes shape or embryos develop. Shapes of intercellular interfaces are closely coupled with the forces resulting from actomyosin interactions, membrane tension, or cell-cell adhesions. Although it is possible to computationally infer cell-cell forces from a mechanical model of collective cell behavior, doing so for temporally evolving forces in a manner robust to digitization difficulties is challenging. Here, we introduce a method for dynamic local intercellular tension estimation (DLITE) that infers such evolution in temporal force with less sensitivity to digitization ambiguities or errors. This method builds upon previous work on single time points (cellular force-inference toolkit). We validate our method using synthetic geometries.
software help: latest

DLO Hi-C
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0602
application sub category: topic_0654
citation: https://doi.org/10.1101/764332
citation: genes11030289
citation: pmcid:PMC7140825
citation: pubmed:32164155
description: DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis | Abstract Background It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (Chromosome Conformation Capture) and its derived methods are now widely applied to investigate genome organizations and gene regulation. Digestion-Ligation-Only Hi-C (DLO Hi-C) is a new technology with high efficiency and effective cost for whole-genome chromosome conformation capture. Results Here, we introduce DLO Hi-C Tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering
feature list: operation 3211
feature list: operation 3798
license: GPL-3.0
operating system: Linux

DMPfold
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0736
application sub category: topic 3474
citation: S41467-019-11994-0
citation: pmcid:PMC6726615
citation: pubmed:31484923
description: Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints | Extending genome-scale de novo protein modelling coverage using iterative deep learning-based prediction of structural constraints | See our paper in Nature Communications for more. Please cite the paper if you use DMPfold | You can also run DMPfold via the PSIPRED web server. This is a good way to get models for a few sequences, but if you want to run DMPfold on many sequences we strongly recommend you run it locally. The server version of DMPfold has restrictions on run time and uses parameters that give faster runs, so should not be used to benchmark DMPfold
feature list: operation_0269
feature list: operation_0303
feature list: operation_0476
license: GPL-3.0

DNA-BOT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0114
application sub category: topic_0196
application sub category: topic_0749
application sub category: topic 3318
application sub category: topic 3895
citation: ysaa010
citation: https://doi.org/10.1101/832139
citation: pmcid:PMC7476404
citation: pubmed:32995552
description: A low-cost, automated DNA assembly platform for synthetic biology. Material for DNA assembly using BASIC on OpenTrons (DNA-BOT). Users looking to implement the DNA-BOT workflow are encouraged to consult the instructions. If you are looking to contribute to this project, please raise an issue or pull request. Otherwise, feel free to reach out to hainesm6
feature list: operation_0310
feature list: operation 3435
license: MIT
software help: DNA BOT instructions v1.0.0.pdf

DNABarcodeCompatibility
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Library
application sub category: topic 3168
application sub category: topic 3314
citation: bty1030
citation: pmcid:PMC6662285
citation: pubmed:30576403
description: R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments.
feature list: operation 3192
feature list: operation 3200
feature list: operation 3745
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: quickStartTutorial.pdf
primary contact: Céline Trébeau

DNA Chisel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
additional type: Web application
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic_0632
application sub category: topic_0654
application sub category: topic 3500
citation: btaa558
citation: https://doi.org/10.1101/2019.12.16.877480
citation: pubmed:32647895
description: DNA Chisel - A versatile sequence optimizer. DNA Chisel is a Python library for optimizing DNA sequences with respect to a set of constraints and optimization objectives. It comes with over 15 classes of sequence specifications which can be composed to, for instance, codon-optimize genes, meet the constraints of a commercial DNA provider, avoid homologies between sequences, tune GC content, or all of this at once!
feature list: operation 3095
feature list: operation 3096
license: MIT

DNA Rchitect
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic 3169
application sub category: topic 3173
citation: btz608
citation: pmcid:PMC7867998
citation: pubmed:31373608
description: An R based visualizer for network analysis of chromatin interaction data | A Shiny App for visualizing genomic data | Welcome to the github repository for DNA Rchitect, a Shiny App for visualizing genomic data | DNA Rchitect is a Shiny App for visualizing genomic data (HiC, mRNA, ChIP, ATAC etc) in bed, bedgraph, and bedpe formats. HiC (bedpe format) data is visualized with both bezier curves coupled with network statistics and graphs (using an R port of igraph). Shiny Apps are interactive web applications built with R using the shiny R package. Shiny apps are built with R wrappers for HTML, CSS, and JS to run R code in a web browser through a dynamic and reactive user interface that is powered by an underlying NodeJS engine. These apps can be locally hosted from an R session or hosted in the cloud through a ShinyServer
feature list: operation_0337
license: MIT

DNA-methyaltion-based age predictor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3399
citation: S13073-019-0667-1
citation: pmcid:PMC6708158
citation: pubmed:31443728
description: A chronological age predictor based on DNA methylation. Improved precision of epigenetic clock estimates across tissues and its implication for biological ageing.
feature list: operation 3196
feature list: operation 3501
feature list: operation 3891

DNAproDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Workflow
application sub category: topic_0097
application sub category: topic_0154
application sub category: topic_0166
application sub category: topic_0654
application sub category: topic 3542
citation: gkz889
citation: pmcid:PMC7145614
citation: pubmed:31612957
description: An expanded database and web-based tool for structural analysis of DNA-protein complexes. A Database and Web Tool for Structural Analysis of DNA-Protein Complexes. DNAproDB automatically lays out nucleotide and residue interactions maps elegantly. Use the form below to search DNAproDB. DNAproDB is processing pipeline, web server and database which aims to assist researchers in performing structural analysis of DNA-protein complexes. DNAproDB is a database, structure processing pipeline and web-based visualization tool which makes structural analysis of DNA-protein complexes easy
feature list: operation_0570
feature list: operation 2421
feature list: operation 2422
feature list: operation 2488
feature list: operation 2939
software help: documentation.html

DNAscan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3316
application sub category: topic 3673
application sub category: topic 3676
citation: s12859-019-2791-8
citation: pmcid:PMC6487045
citation: pubmed:31029080
contributor: Dr Alfredo Iacoangeli
contributor: Dr Stephen J Newhouse
description: Personal computer compatible NGS analysis, annotation and visualisation.
feature list: operation_0337
feature list: operation 3196
feature list: operation 3227
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: KCL IoPPN: NIHR BRC-MH Bioinformatics Group

DNCON2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0160
application sub category: topic 3174
application sub category: topic 3474
citation: btz679
citation: pmcid:PMC7703788
citation: pubmed:31504181
description: Analysis of several key factors influencing deep learning-based inter-residue contact prediction | Deep convolutional neural networks for protein contact map prediction | Web-server and datasets at http://sysbio.rnet.missouri.edu/dncon2/ | We tested in Ubuntu becasue the tool 'FreeContact' is easier to install in a Debian system. If you would like to install DNCON2 in some other operating systems, first test if 'FreeContact' can be installed in it. If, for some reason, you do not have a Ubuntu machine, and cannot install FreeContact, you can still use DNCON2. With just a few code updates you can skip using the FreeContact tool. You will get slightly less precise results
feature list: operation_0272
feature list: operation_0303
feature list: operation_0476
license: GPL-3.0

DNLC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0634
citation: S12859-019-3046-4
citation: pmcid:PMC6929334
citation: pubmed:31874600
description: differential network local consistency analysis. Using Local Moran's I for detection of differential network local consistency
feature list: operation 2497
feature list: operation 3463
license: GPL-2.0
software help: DNLC.pdf

DNA Methylation Interactive Visualization Database (DNMIVD)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0654
application sub category: topic 2640
application sub category: topic 3295
application sub category: topic 3518
application sub category: topic 3674
citation: gkz830
citation: pmcid:PMC6943050
citation: pubmed:31598709
description: DNMIVD is a comprehensive annotation and interactive visualization database for DNA methylation profile of diverse human cancer constructed with high throughput microarray data from TCGA and GEO databases, and it also integrates some data from Pancan-meQTL and HACER databases. Overall, DNMIVD mainly contains the following important resources:. DNA methylation is strongly related to cancer, currently, no resource integratively provides the DNA methylation based diagnostic and prognostic models, e-mQTL (expression–methylation quantitative trait loci), pathway-meQTL (pathway activity-methylation quantitative trait loci), differentially variable and differentially methylated CpGs, survival analysis, as well as functional epigenetic modules for different cancers, which are valuable information for researchers to explore DNA methylation profile from different aspects in cancer
feature list: operation 3186
feature list: operation 3206
feature list: operation 3207

DNSS2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0082
application sub category: topic_0160
application sub category: topic 3542
citation: https://doi.org/10.1101/639021
description: Improved ab initio protein secondary structure prediction using advanced deep learning architectures.
feature list: operation_0468
feature list: operation_0469
feature list: operation_0470
is accessible for free: true
license: Unlicense
operating system: Linux
software help: README.md
primary contact: Jianlin Cheng

DO-MS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: acs.jproteome.9b00039
citation: pmcid:PMC6737531
citation: pubmed:31081635
description: Data-Driven Optimization of Mass Spectrometry Methods.
feature list: operation 2428
feature list: operation 3631
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: getting-started
software help: getting-started-application
software help: getting-started-command-line
primary contact: Nikolai Slavov

DOGMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0736
application sub category: topic 3308
citation: GKZ366
citation: btw231
citation: pmcid:PMC6602495
citation: pubmed:27153665
citation: pubmed:31076763
description: Domain-based transcriptome and proteome quality assessment.
feature list: operation 3218
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: https://orcid.org/0000-0002-2416-9842

DORMAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0625
application sub category: topic 3068
application sub category: topic 3407
citation: TCBB.2019.2944905
citation: pubmed:31581093
description: Database Of Reconstructed MetAbolic Networks. We apologize for the inconvenience, but it appears that an internal error has occurred in the Dorman system. If this is the first time you have encountered this message, please use the Back button on your browser and try your last action again. If you are receiving this message repeatedly, please send an e-mail to (aec51 [at] case [dot] edu) with a detailed description of what you were doing when this message occurred so that we may try and resolve this issue. Thank you!
feature list: operation_0224
feature list: operation 3083
feature list: operation 3660

DOVE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic 3423
application sub category: topic 3512
application sub category: topic 3577
citation: mgg3.510
citation: pmcid:PMC6382494
citation: pubmed:30450799
description: DMD Open-access Variant Explorer (DOVE) - web-based aid for DMD variant interpretation which additionally reports variant-specific predicted molecular eligibility for therapy.
feature list: operation_0446
feature list: operation 3225
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: dmd-interpreter
primary contact: Mitch Bailey

DPre
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
citation: BTZ789
citation: pubmed:31621827
description: DPre: Computational identification of differentiation bias and genes underlaying cell type conversions. DPre is a bioinformatic tool that enables the user to explore cell type conversion/ differentiation experiments. DPre may take the expression or the differentially regulated genes of the samples to rate transcriptional similarity with a reference dataset, the targets.
feature list: operation_0337
feature list: operation 2495
feature list: operation 3629
license: MIT

DQueST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0218
application sub category: topic 3063
application sub category: topic 3379
citation: OCZ121
citation: pmcid:PMC6798577
citation: pubmed:31390010
description: DQueST is a web applciation for reducing information overload for trial seekers using dynamic questionnaires.
feature list: operation 3280

DR-thermo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3318
application sub category: topic 3489
citation: BTZ741
citation: pubmed:31584610
description: Thermodynamically Consistent Estimation of Gibbs Free Energy from Data. The DR-thermo algorithm can be used to curate experimental thermodynamic data from different sources to generate reliable data-banks such that all measurements are modified to be thermodynamically consistent and any missing reaction or formation Gibbs energies can be predicted either directly or using group contributions.
feature list: operation 3557
feature list: operation 3659
feature list: operation 3799
license: MIT

DRAMP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic 3301
application sub category: topic 3379
citation: S41597-019-0154-Y
citation: pmcid:PMC6692298
citation: pubmed:31409791
description: updated data repository of antimicrobial peptides | Browse, Create and Mining Antimicrobial Peptides | 157 new entries are added to in DRAMP. 33 entries are natural AMPs including 31 animal AMPs and 2 plant AMPs. 124 entries are synthetic AMPs | A brief introduction to DRAMP database | DRAMP database is an information portal to biological active peptides. Peptides in this database come from three sources : Public databases (Swiss-Prot, PDB, PubMed), Clinical antimicrobial peptides (preclinical and clinical) and Patents | DRAMP(Data repository of antimicrobial peptides) is an open-access and manually curated database harboring diverse annotations of AMPs including sequences, structures, activities, physicochemical, patent, clinical and reference information | We are responsible for maintaining the website daily and updating the database regularly
feature list: operation 3431
feature list: operation 3482
feature list: operation 3646
software help: readme.php

DRAMS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic 3170
application sub category: topic 3673
citation: https://doi.org/10.1101/831537
citation: journal.pcbi.1007522
citation: pmcid:PMC7179940
citation: pubmed:32282793
description: A tool to Detect and Re-Align Mixed-up Samples based on multi-omics data. Need at least three types of -omics data to run this tool.
feature list: operation_0282
feature list: operation 3196
feature list: operation 3431
feature list: operation 3659
feature list: operation 3802

DREAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 3855
citation: J.EJMP.2019.06.013
citation: pubmed:31515012
description: A user-friendly program for the analyses of radiation-induced biological responses utilizing established deterministic models at cell population and organ scales | PURPOSE:To develop a user-friendly program for biological modeling to analyze radiation-induced responses at the scales of the cell population and organ. METHODS:The program offers five established cell population surviving fraction (SF) models to estimate the SF and the relative biological effectiveness (RBE) from clonogenic assay data, and two established models to calculate the normal tissue complication probability (NTCP) and tumor control probability (TCP) from radiation treatment plans. Users can also verify the results with multiple types of quantitative analyses and graphical representation tools

DROPA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 3168
application sub category: topic 3512
citation: S12859-019-3009-9
citation: pmcid:PMC6685255
citation: pubmed:31387525
description: DRIP-seq optimized peak annotator | DROPA is a fully customizable peak-annotation tool optimized for DRIP-seq peaks, which allows a finest gene annotation based on gene expression information. Its output can easily be integrated into pipelines to perform downstream analyses, while useful and informative summary plots and statistical enrichment tests can be produced. Although it is developed for R-loop mapping, DROPA can also be used to annotate other genomic sequencing data as in the case of Histone marks IP-seq, DNAse-seq, FAIRE-seq
feature list: operation 3215
feature list: operation 3222
feature list: operation 3501
license: MIT

DRUDIT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3047
application sub category: topic 3336
citation: BTZ783
citation: pubmed:31605102
description: DRUDIT, Web-Based DRUgs DIscovery Tools to Design Small Molecules as Modulators of Biological Targets.
feature list: operation 3761
software help: DRUDIT user manual.pdf

DNA Readout Viewer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0160
application sub category: topic_0166
citation: btz906
citation: pmcid:PMC7141859
citation: pubmed:31793988
description: DNA Readout Viewer is a free on-line service providing novel and intuitive visualisation modes for displaying sequence specific DNA-protein interactions.
feature list: operation_0239
feature list: operation_0337
feature list: operation 3894
software help: about drv.html
software help: quick start guide.html

DRfit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0821
application sub category: topic 3336
application sub category: topic 3855
citation: s12859-019-2891-5
citation: pmcid:PMC6528253
citation: pubmed:31113359
description: Tool for the analysis of discrete data from multi-well plate assays.
feature list: operation_0337
feature list: operation 1812
feature list: operation 3435
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial
software help: http://www.structuralchemistry.org/ts/download2.php

DSEA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic_0602
citation: btv536
citation: pmcid:PMC4795590
citation: pubmed:26415724
description: Drug-Set Enrichment Analysis (DSEA) - computational method based on drug-induced gene expression profiles, which is able to identify the molecular pathways that are targeted by most of the drugs in the set.
feature list: operation 3501
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: about.php
primary contact: Diego Carrella
primary contact: Diego di Bernardo
primary contact: Francesco Napolitano

DSIMB tools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic 1317
description: A collection of databases, tools and web servers for structural biology.

DTA-SiST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3320
application sub category: topic 3512
citation: S12859-019-3272-9
citation: pmcid:PMC6929406
citation: pubmed:31874618
description: de novo transcriptome assembly by using simplified suffix trees. DTA-SiST: a novel radical framework for de novo transcriptome assembly based on suffix trees. The RNA-seq has revolutionized our ability to transcripts reconstruction
feature list: operation_0524
feature list: operation 3258
feature list: operation 3472

DTCLab
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0209
application sub category: topic 2258
citation: ACSOMEGA.8B01647
citation: ACSOMEGA.8B01834
citation: pmcid:PMC6645132
citation: pmcid:PMC6645227
citation: pubmed:31458051
citation: pubmed:31459245
description: How Precise Are Our Quantitative Structure-Activity Relationship Derived Predictions for New Query Chemicals? | QSPR Modeling of the Refractive Index for Diverse Polymers Using 2D Descriptors | QSAR Model Development Using DTC Lab. Software Tools | DTC lab - Software Tools - DTC lab is working in the field of molecular modelling mainly using different QSAR methodologies in various diverse area such as drug designing, toxicity, anti-oxidant studies etc | Drug Theoretics and Cheminformatics Laboratory | *Genetic Algorithm(MAE-based Fitness Function) | *Intelligent Consensus Predictor
feature list: operation_0337
feature list: operation 3799
feature list: operation 3891

DTI-CDF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic 3336
application sub category: topic 3375
application sub category: topic 3474
citation: BBZ152
citation: pubmed:31885041
description: A cascade deep forest model towards the prediction of drug-target interactions based on hybrid features. Drug-target interactions (DTIs) play a crucial role in target-based drug discovery and development
feature list: operation_0269
feature list: operation_0303
feature list: operation 3435

DUETT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0099
application sub category: topic_0749
citation: btz449
citation: pmcid:PMC6954663
citation: pubmed:31389563
description: DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data | MOTIVATION:RNA molecules can undergo complex structural dynamics, especially during transcription, which influence their biological functions. Recently developed high-throughput chemical probing experiments that study RNA cotranscriptional folding generate nucleotide-resolution 'reactivities' for each length of a growing nascent RNA that reflect structural dynamics. However, the manual annotation and qualitative interpretation of reactivity across these large datasets can be nuanced, laborious, and difficult for new practitioners. We developed a quantitative and systematic approach to automatically detect RNA folding events from these datasets to reduce human bias error, standardize event discovery, and generate hypotheses about RNA folding trajectories for further analysis and experimental validation
feature list: operation_0244
feature list: operation_0303
feature list: operation 3799

DVASS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0099
citation: GKZ427
citation: pmcid:PMC6582333
citation: pubmed:31106330
description: Algorithm based on the distance variation allowed by secondary structure (DVASS), which ranks restraints according to their importance to RNA tertiary structure prediction.
feature list: operation_0278
feature list: operation_0502
feature list: operation 2441
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README
primary contact: https://orcid.org/0000-0002-8225-4025

DaReUS-Loop
type: SoftwareApplication
input: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1476
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
output: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1476
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2275
application sub category: topic 3542
citation: s41598-018-32079-w
citation: gkz403
citation: pmcid:PMC6135855
citation: pmcid:PMC6602439
citation: pubmed:30209260
citation: pubmed:31114872
description: Web server for the (re-)modeling of loops in homology models. It follows a data-based approach, identifying loop candidates by mining the complete set of experimental structures available in the Protein Data Bank.
feature list: operation_0481
is accessible for free: true
license: Freeware
software help: DaReUS-Loop
software version: 1.0
primary contact: Pierre Tufféry
primary contact: Sjoerd de Vries

Dashing
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic 3174
application sub category: topic 3361
citation: S13059-019-1875-0
citation: pmcid:PMC6892282
citation: pubmed:31801633
description: Fast and accurate genomic distances using HyperLogLog. dashing sketches and computes distances between fasta and fastq data.
feature list: operation 3211
feature list: operation 3472
feature list: operation 3695
license: GPL-3.0

DatView
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2828
application sub category: topic 3794
author: Natasha Stander
citation: S1600576719012044
citation: pmcid:PMC6878877
citation: pubmed:31798364
description: A graphical user interface for visualizing and querying large data sets in serial femtosecond crystallography. DatView displays plots of tabular data and syncs selections across plots. It was initially developed for serial crystallography data analysis with CrystFEL output files and includes a frame viewer for displaying 1D and 2D data from HDF5/CXI files.
feature list: operation_0337
feature list: operation 3359
feature list: operation 3436
feature list: operation 3695
feature list: operation 3802
software help: overview
software help: Tutorial+2019

DataDiscovery
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Keyword
  type: FormalParameter
  additional type: data_0968
output: Data reference
  type: FormalParameter
  additional type: data 2093
output: Database search results
  type: FormalParameter
  additional type: data 2080
output: Identifier
  type: FormalParameter
  additional type: data_0842
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
additional type: Web application
additional type: Web service
application sub category: topic_0091
application sub category: topic_0610
application sub category: topic_0780
application sub category: topic 3071
application sub category: topic 3810
citation: hortres.2016.56
citation: s13059-018-1491-4
citation: plantgenome2015.06.0038
description: DataDiscovery aims at providing researchers a simple and fast access to relevant biological data using specific keywords and easy to use filters. This tool is expected to be easily customizable for specific filters, environments, or data schemas. Its current implementations supported by URGI are: WheatIS, Plant, RARe.
feature list: operation_0227
feature list: operation 2421
feature list: operation 3625
feature list: operation 3908
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
software help: HELP.md
software help: LEGAL-MENTIONS.md
software help: contribute
software help: setup
primary contact: urgi-support

Data Information System (DAISY)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3071
application sub category: topic 3394
application sub category: topic 3571
author: https://orcid.org/0000-0001-6501-0806
author: Jacek Lebioda
author: Kavita Rege
author: Yohan Jarosz
citation: GIZ140
citation: pmcid:PMC6892452
citation: pubmed:31800037
contributor: https://orcid.org/0000-0002-6532-5880
contributor: https://orcid.org/0000-0002-8278-1618
contributor: Christophe Trefois
contributor: Sandrine Munoz
contributor: Vilem Ded
description: DAISY is an open-source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement.
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.1.0
primary contact: https://orcid.org/0000-0002-2224-0780
primary contact: Regina Becker

Data Stewardship Wizard
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0605
author: https://orcid.org/0000-0001-7525-9218
author: https://orcid.org/0000-0003-0103-8468
author: Jan Slifka
citation: j.ipm.2020.102480
citation: dint a 00043
citation: dsj-2019-059
contributor: https://orcid.org/0000-0003-2980-4400
contributor: Rob Hooft
description: The Data Stewardship Wizard is an international project to help serious researchers and data stewards with building smart Data Management Plans for FAIR Open Science.
is accessible for free: true
license: Apache-2.0
software help: guide.ds-wizard.org
software help: roadmap
software help: deployment
primary contact: https://orcid.org/0000-0001-7525-9218
primary contact: https://orcid.org/0000-0003-2980-4400

Datab.io
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0108
application sub category: topic_0203
citation: https://doi.org/10.1101/768077
citation: s13104-020-05038-w
citation: pmcid:PMC7110638
citation: pubmed:32238171
description: Automated Gene Data Integration with Databio | Automated data transformation for bioinformatics | Automated data integration tools | A simple Gene ID mapping service for Bioinformatics. Upload a gene-oriented data set, we'll automatically detect the identifiers in use, and offer to convert them to match other providers in just a few clicks | A web portal that does automated identifier translation for bioinformatics
feature list: operation 1812
feature list: operation 2422
feature list: operation 3282
operating system: Linux
operating system: Mac
operating system: Windows

Datastorr
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0610
application sub category: topic_0769
application sub category: topic 3068
citation: GIZ035
citation: pmcid:PMC6506717
citation: pubmed:31042286
description: Workflow and package for delivering successive versions of 'evolving data' directly into R.
feature list: operation 2422
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: 0000-0002-9814-092X
primary contact: Rich FitzJohn

De-smokeGCN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3384
application sub category: topic 3421
application sub category: topic 3474
author: https://orcid.org/0000-0002-4985-9516
citation: TMI.2019.2953717
citation: pubmed:31751268
description: Generative cooperative networks for joint surgical smoke detection and removal in order to remove surgical smoke and improve the quality of intra-operative imaging and reduce hazards in image-guided surgery. This is a highly desirable post-process for many clinical applications.
feature list: operation 3443
feature list: operation 3799
feature list: operation 3891
license: GPL-3.0

DeLinker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0209
application sub category: topic 2275
application sub category: topic 3047
application sub category: topic 3303
application sub category: topic 3474
citation: acs.jcim.9b01120
citation: https://doi.org/10.1101/830497
citation: pmcid:PMC7189367
citation: pubmed:32195587
description: Deep Generative Models for 3D Compound Design. This repository contains our implementation of Deep Generative Models for 3D Compound Design (DeLinker). We provide two settings of DeLinker. The first setting generates linkers with the same number of atoms as the reference molecule. The second setting generates linkers with a specified number of atoms
feature list: operation 3216
feature list: operation 3435
feature list: operation 3891

DeTerm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3474
citation: GTC.12700
citation: pubmed:31095815
description: Software for automatic detection of neuronal dendritic branch terminals via an artificial neural network.
feature list: operation 3450
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: Home

DecoMetDIA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3172
application sub category: topic 3370
application sub category: topic 3520
citation: ACS.ANALCHEM.9B02655
citation: pubmed:31436405
description: Deconvolution of Multiplexed MS/MS Spectra for Metabolite Identification in SWATH-MS-Based Untargeted Metabolomics | DecoMetDIA was developed to process SWATH-MS based data for metabolomics.
feature list: operation 3629
feature list: operation 3637
feature list: operation 3803

DecontaMiner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3168
application sub category: topic 3173
application sub category: topic 3308
citation: s12859-019-2684-x
citation: pmcid:PMC6472186
citation: pubmed:30999839
description: Tool for detecting contaminating organisms in human unmapped sequences.
feature list: operation 3187
feature list: operation 3219
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: download user guide.php

DecoyDeveloper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: acs.jproteome.9b00203
citation: pmcid:PMC6768553
citation: pubmed:31129958
description: On-demand decoy glycopeptide generator that can produce a high volume of decoys with low mass differences.
feature list: operation_0417
feature list: operation 2929
feature list: operation 3644
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

DeePathology
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3308
application sub category: topic 3474
citation: S41598-019-52937-5
citation: pmcid:PMC6848155
citation: pubmed:31712594
description: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome. Tissue and Cancer Type Identification using Deep Neural Networks. Authors: Behrooz Azarkhalili, Ali Saberi, Hamidreza Chitsaz, Ali Sharifi-Zarchi
feature list: operation 3435
feature list: operation 3792

Deep-Z
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic_0621
application sub category: topic 3382
application sub category: topic 3474
citation: S41592-019-0622-5
citation: pubmed:31686039
description: Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning. DeepZ Plugin Release_v1.3 – Google Drev. Three-dimensional propagation and time-reversal of fluorescence images. Neural network learns fluorescence wave propagation and time-reversal to propagate a 2D fluorescence image onto user-defined 3D surfaces, enabling 3D imaging of fluorescent samples using a single 2D image, without mechanical scanning, additional hardware, or a trade-off of resolution or speed. For details, refer to our publication "Three-dimensional propagation and time-reversal of fluorescence images" [1]. (Video below: 3D reconstruction of a C. elegans using Deep-Z inference)
feature list: operation 3450
feature list: operation 3457
feature list: operation 3552
software help: edit
software help: 1ZXPAf9TIikLjk5PEr0Kn-mN9xhpqahwm

DeepAttentionPan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0199
application sub category: topic 2830
application sub category: topic 3474
citation: https://doi.org/10.1101/830737
description: Attention mechanism-based deep learning pan-specific model for interpretable MHC-I peptide binding prediction. Deep learning prediction of MHC-I peptide binding with attention mechanism. Please download the full folder of "DeepAttentionPan_Code" to run the programs, or you may need to configure some directory paths. Usage: the codes can be used to train our models, output results on the testing set, output positional attention weights for chosen group of peptides. And they also can be used to test on single hla-peptide pair input from the command line.
feature list: operation_0252
feature list: operation 2492
feature list: operation 3439

DeepBGC
type: SoftwareApplication
input: DNA sequence
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  encoding format: format 1936
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3474
citation: GKZ654
citation: pmcid:PMC6765103
citation: pubmed:31400112
description: A deep learning genome-mining strategy for biosynthetic gene cluster prediction | BGC Detection and Classification Using Deep Learning | DeepBGC: Biosynthetic Gene Cluster detection and classification | DeepBGC detects BGCs in bacterial and fungal genomes using deep learning. DeepBGC employs a Bidirectional Long Short-Term Memory Recurrent Neural Network and a word2vec-like vector embedding of Pfam protein domains. Product class and activity of detected BGCs is predicted using a Random Forest classifier
feature list: operation_0306
feature list: operation 3803
license: MIT

DeepBindRG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic 2275
application sub category: topic 3474
citation: PEERJ.7362
citation: pmcid:PMC6661145
citation: pubmed:31380152
description: A deep learning based method for estimating effective protein-ligand affinity.
feature list: operation_0482
license: MIT

DeepCC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3518
citation: S41389-019-0157-8
citation: pmcid:PMC6697729
citation: pubmed:31420533
description: A novel deep learning-based framework for cancer molecular subtype classification | a deep learning-based framework for cancer classification | After training, now you can use your DeepCC model to classify new sample(s). DeepCC can classify samples in a data set, as well as individual samples. The input data should be in the same format as above gene expression profile(s)
feature list: operation 2436
license: MIT

DeepCINAC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Workflow
application sub category: topic 2229
application sub category: topic 3382
application sub category: topic 3474
citation: https://doi.org/10.1101/803726
citation: ENEURO.0038-20.2020
citation: pmcid:PMC7438055
citation: pubmed:32699072
description: A deep-learning-based Python toolbox for inferring calcium imaging neuronal activity based on movie visualization. Abstract Two-photon calcium imaging is now widely used to indirectly infer multi neuronal dynamics from changes in fluorescence of an indicator. However, state of the art computational tools are not optimized for the analysis of highly active neurons in densely packed regions such as the CA1 pyramidal layer of the hippocampus during early postnatal stages of development. Indeed, the reliable inference of single cell activity is not achieved by the latest analytical tools that often lack proper benchmark measurements. To meet this challenge, we first developed a graphical user interface allowing for a precise manual detection of all calcium transients from detected neurons based on the visualization of the calcium imaging movie. Then, we analyzed our movies using a convolutional neural network with an attention process and a bidirectional long-short term memory network
feature list: operation_0337
feature list: operation 3450
license: MIT
software help: index.html
software help: install.html
software help: tutorial gui.html

DeepCLIP
type: SoftwareApplication
input: Nucleic acid sequence
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input: Sequence coordinates
  type: FormalParameter
  additional type: data 2012
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output: Score
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  encoding format: format 2330
  encoding format: format 3464
output: Mathematical model
  type: FormalParameter
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  encoding format: format 4002
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web service
application sub category: topic_0128
application sub category: topic 3474
application sub category: topic 3794
author: https://orcid.org/0000-0001-8076-5035
author: https://orcid.org/0000-0002-5315-8325
author: Alexander Gulliver Bjørnholt Grønning
citation: gkaa530
citation: https://doi.org/10.1101/757062
citation: pmcid:PMC7367176
citation: pubmed:32558887
description: Predicting the effect of mutations on protein-RNA binding with Deep Learning | This repository contains all DeepCLIP Python code | A context-aware neural network for modeling and predicting protein binding to nucleic acids using only sequence input | DeepCLIP is a neural network with shallow convolutional layers connected to a bidirectional LSTM layer
feature list: operation_0441
feature list: operation 3901
feature list: operation 3902
is accessible for free: true
license: MIT
operating system: Linux
software help: README.md
primary contact: https://orcid.org/0000-0002-5315-8325

Deep gene compound profiler (DeepCOP)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0204
application sub category: topic 2640
citation: BTZ645
citation: pubmed:31504186
description: Deep Learning-Based Approach to Predict Gene Regulating Effects of Small Molecules | MOTIVATION:Recent advances in the areas of bioinformatics and chemogenomics are poised to accelerate the discovery of small-molecule regulators of cell development. Combining large genomics and molecular data sources with powerful deep learning techniques has the potential to revolutionize predictive biology. In this study, we present Deep Compound Profiler (DeepCOP), a deep learning based model that can predict gene regulating effects of low-molecular weight compounds. This model can be used for direct identification of a drug candidate causing a desired gene expression response, without utilizing any information on its interactions with protein target(s)
feature list: operation 3501
license: MIT

DeepCalpain
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic 2640
application sub category: topic 3534
citation: FGENE.2019.00715
citation: pmcid:PMC6694742
citation: pubmed:31440276
description: Precise Prediction of Calpain Cleavage Sites and Their Aberrance Caused by Mutations in Cancer | SWISS-MODEL is a fully automated protein structure homology-modelling server. The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide | DeepCalpain is a web server developed for understanding the enzyme-specific cleavage for calpains including m-calpain and μ-calpain
feature list: operation_0267
feature list: operation_0417
feature list: operation_0422

DeepCirCode
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3320
application sub category: topic 3474
application sub category: topic 3512
citation: BTZ382
citation: pubmed:31077303
description: R package for deep learning of the back-splicing code for circular RNA formation.
feature list: operation_0264
feature list: operation 1812
feature list: operation 3501
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Jun Wang
primary contact: Liangjiang Wang

DeepCleave
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0821
application sub category: topic 3534
citation: btz721
citation: pmcid:PMC8215920
citation: pubmed:31566664
description: A deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites | Proteases are enzymes that cleave target substrate proteins by catalyzing the hydrolysis of peptide bonds between specific amino acids. While the functional proteolysis regulated by proteases plays a central role in the 'life and death' process of proteins, many of the corresponding substrates and their cleavage sites were not found yet. Availability of accurate predictors of the substrates and cleavage sites would facilitate understanding of proteases' functions and physiological roles. Deep learning is a promising approach for the development of accurate predictors of substrate cleavage events. RESULTS:We propose DeepCleave, the first deep learning-based predictor of protease-specific substrates and cleavage sites. DeepCleave uses protein substrate sequence data as input and employs convolutional neural networks with transfer learning to train accurate predictive models
feature list: operation_0366
feature list: operation_0422

DeepDBP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0121
application sub category: topic_0654
application sub category: topic 3169
application sub category: topic 3474
citation: j.imu.2020.100318
citation: https://doi.org/10.1101/829432
description: Deep Neural Networks for Identification of DNA-binding Proteins.
feature list: operation 3767
feature list: operation 3900
feature list: operation 3901

DeepDNA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic 2269
application sub category: topic 2815
application sub category: topic 3474
application sub category: topic 3796
citation: S40246-019-0225-3
citation: pmcid:PMC6805717
citation: pubmed:31639043
description: A hybrid convolutional and recurrent neural network for compressing compression human mitochondrial genomes. DeepDNA, a novel unified model called deepDNA that combines the convolutional neural network (CNN) with the long short-term memory network (LSTM) for compressing human mitochondrial genome sequences. The experiment has shown that out method deepDNA is able to learn sequence local features through a convolutional layer, and to learn higher level representations of long-term sequences dependencies through a long short-term memory network (LSTM) layer. We evaluated the learned genome sequences representations model on human mitochondrial genome sequences compressing tasks and achieved a satisfactory result.
feature list: operation 2428
feature list: operation 3435
feature list: operation 3695
license: MIT

DeepDRBP-2L
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0099
application sub category: topic_0121
application sub category: topic_0203
application sub category: topic_0634
application sub category: topic 3474
citation: TCBB.2019.2952338
citation: pubmed:31722485
description: A new genome annotation predictor for identifying DNA binding proteins and RNA binding proteins using Convolutional Neural Network and Long Short-Term Memory. In this study, we proposed a new computational predictor called DeepDRBP-2L for identifying DBPs, RBPs and DRBPs. DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) are two kinds of crucial proteins, which are involved in various cellule activities and associated with many diseases
feature list: operation 3900
feature list: operation 3901

DeepEP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3474
citation: S12859-019-3076-Y
citation: pmcid:PMC6886168
citation: pubmed:31787076
description: A deep learning framework for identifying essential proteins. DeepEP is a deep learning framework to automatically predict essential proteins using PPI network and gene expression data.
feature list: operation 2454
feature list: operation 2495
feature list: operation 3439
license: MIT

DeepHF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0099
application sub category: topic 3168
application sub category: topic 3474
citation: S41467-019-12281-8
citation: pmcid:PMC6753114
citation: pubmed:31537810
description: Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning | Core code for the DeepHF prediction tool | SpCas9 & Base Editor Efficiency Prediction | This tool provides guide designs for Wild-type SpCas9, two highly specific Cas9 mutants(eSpCas9 (1.1) and SpCas9-HF1) and base editors (AncBE4max, ABEmax)
feature list: operation_0308
feature list: operation 3096
feature list: operation 3216

DeepHLApan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 2830
application sub category: topic 3474
application sub category: topic 3520
citation: FIMMU.2019.02559
citation: pmcid:PMC6838785
citation: pubmed:31736974
description: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity. A deep learning approach for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC. DeepHLApan Server – A deep learning approach used for neoantigen prediction. DeepHLApan is a deep learning approach used for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC. A deep learning approach used for neoantigen prediction. DeepHLApan is a deep learning approach used for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC. The stand-alone software is available in github
feature list: operation_0252
feature list: operation_0331
feature list: operation_0416
license: GPL-2.0

DeepImageJ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic_0102
application sub category: topic_0605
application sub category: topic 3382
application sub category: topic 3398
application sub category: topic 3474
citation: https://doi.org/10.1101/799270
description: A user-friendly plugin to run deep learning models in ImageJ. Websites for you and your projects, hosted directly from your GitHub repository. Just edit, push, and your changes are live. DeepImageJ is a user-friendly plugin that enables the use of a variety of pre-trained deep learning models in ImageJ and Fiji. The plugin bridges the gap between deep learning and standard life-science applications. DeepImageJ runs image-to-image operations on a standard CPU-based computer and does not require any deep learning expertise.
feature list: operation 3096
feature list: operation 3435
feature list: operation 3629
license: GPL-3.0

DeepImpute
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3474
application sub category: topic 3512
citation: S13059-019-1837-6
citation: pmcid:PMC6798445
citation: pubmed:31627739
description: An accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data. An accurate and efficient deep learning method for single-cell RNA-seq data imputation.
feature list: operation 2940
feature list: operation 3557
license: MIT

DeepInsight
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3304
application sub category: topic 3382
application sub category: topic 3421
application sub category: topic 3474
citation: https://doi.org/10.1101/871848
description: A general framework for interpreting wide-band neural activity. DeepInsight is a toolbox for the analysis and interpretation of wide-band neural activity and can be applied on unsorted neural data. This means the traditional step of spike-sorting can be omitted and the raw data can be used directly as input, providing a more objective way of measuring decoding performance.
feature list: operation_0337
feature list: operation 3659
license: MIT

DeepLigand
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2830
citation: BTZ330
citation: pmcid:PMC6612839
citation: pubmed:31510651
description: An accurate prediction of MHC class I ligands using peptide embedding | The 5-fold cross-validation split used in the paper can be downloaded from here. The DeepLigand model provided in this repository is trained on all the five folds combined
feature list: operation_0252
license: MIT

Deep learning for Metagenome Assembly Error Detection (DeepMAsED)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3837
citation: https://doi.org/10.1101/763813
description: Evaluating the quality of metagenomic assemblies
feature list: operation_0310
feature list: operation 2495
feature list: operation 3180
license: MIT

DeepMF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3308
citation: https://doi.org/10.1101/744706
citation: s12859-019-3291-6
citation: pmcid:PMC6933662
citation: pubmed:31881818
description: Deciphering the Latent Patterns in Omics Profiles with a Deep Learning Method | Deciphering the Hidden Patterns on Transcriptome Profiles with a Deep Learning Fashion
feature list: operation 3557
feature list: operation 3891

DeepMSA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic_0082
application sub category: topic_0160
application sub category: topic 3174
application sub category: topic 3474
citation: btz863
citation: pmcid:PMC7141871
citation: pubmed:31738385
description: Constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. deep multiple sequence alignment generation. DeepMSA is a composite approach to generate high quality multiple sequence alignment with large alignment depth and diverse sequence sources by merging sequences from whole-genome sequence databases (Uniclust30 and UniRef90) and from metagenome database (Metaclust). Large-scale benchmark data show that DeepMSA profiles consistently improves contact prediction, secondary structure prediction, and threading over default HHblits or PSI-BLAST profiles
feature list: operation_0267
feature list: operation_0272
feature list: operation_0292
feature list: operation_0303
feature list: operation 3192

DeepMSPeptide
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: BTZ708
citation: pubmed:31529040
description: The protein detection and quantification using high-throughput proteomic technologies is still challenging due to the stochastic nature of the peptide selection in the mass spectrometer, the difficulties in the statistical analysis of the results and the presence of degenerated peptides. However, considering in the analysis only those peptides that could be detected by mass spectrometry (MS), also called proteotypic peptides, increases the accuracy of the results. Several approaches have been applied to predict peptide detectability based on the physicochemical properties of the peptides. In this manuscript we present DeepMSPeptide, a bioinformatic tool that uses a deep learning method to predict proteotypic peptides exclusively based on the peptide amino acid sequences
feature list: operation_0252
feature list: operation_0418
feature list: operation 2929
license: MIT

DeepMicro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
application sub category: topic 3305
application sub category: topic 3400
application sub category: topic 3474
application sub category: topic 3697
citation: s41598-020-63159-5
citation: https://doi.org/10.1101/785626
citation: pmcid:PMC7138789
citation: pubmed:32265477
description: Deep representation learning for disease prediction based on microbiome data. DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.
feature list: operation 3200
feature list: operation 3359
feature list: operation 3891
license: MIT

DeepMir
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3474
application sub category: topic 3512
citation: S12859-019-3279-2
citation: pmcid:PMC6933638
citation: pubmed:31881831
description: Fast and accurate microRNA search using CNN.
feature list: operation_0463
feature list: operation 2421
feature list: operation 3792

DeepMito
type: SoftwareApplication
input: Protein sequence (raw)
  type: FormalParameter
  additional type: data 2974
  encoding format: format 2200
output: Sequence report
  type: FormalParameter
  additional type: data 2955
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0140
citation: btz512
citation: s12859-020-03617-z
citation: pmcid:PMC6956790
citation: pmcid:PMC7493403
citation: pubmed:31218353
citation: pubmed:32938368
description: Predictor of protein sub-mitochondrial localization based on deep learning
feature list: operation 2489
feature list: operation 3672
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: deepmito
software version: 1.0

DeepPASTA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 3474
application sub category: topic 3512
citation: btz283
citation: pmcid:PMC6853695
citation: pubmed:31081512
description: Deep neural network based polyadenylation site analysis.
feature list: operation_0267
feature list: operation_0278
feature list: operation_0428
is accessible for free: true
license: Unlicense
operating system: Linux
software help: README.md
primary contact: Ashraful Arefeen

DeepPPISP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic 3474
application sub category: topic 3510
application sub category: topic 3542
citation: BTZ699
citation: pubmed:31593229
description: Protein-protein interaction site prediction through combining local and global features with deep neural networks. PPI sites prediction through combining local and global features with deep neural networks. DeepPPISP: Protein-protein interaction sites prediction through combining local and global features with deep neural networks. You can run the train.py file to train DeepPPISP and use the predcit.py file to see the predictive resluts. If you want to tune some hyper-parameters, you can change some values of hyper-parameters in config.py in utils folder. The PSSMs, raw sequences, secondary structures and labels are given in data_cache folder.
feature list: operation 2492
feature list: operation 3092
feature list: operation 3439
feature list: operation 3899
license: MIT

DeepPVP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic 3676
citation: s12859-019-2633-8
citation: pmcid:PMC6364462
citation: pubmed:30727941
description: Phenotype-based variant prioritization method that combined automated inference with deep neural networks to identify the likely causative variants in whole exome or whole genome sequence data.
feature list: operation 3196
feature list: operation 3225
feature list: operation 3227
is accessible for free: true
license: BSD-4-Clause
operating system: Linux
operating system: Mac
primary contact: Bio-Ontology Research Group

DeepPheno
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3474
application sub category: topic 3577
citation: https://doi.org/10.1101/839332
citation: journal.pcbi.1008453
citation: pmcid:PMC7710064
citation: pubmed:33206638
description: DeepPheno is a method for predicting gene-phenotype (HPO classes) associations from gene functional annotations (GO classes). Predicting single gene knockout phenotypes.
feature list: operation 2454
feature list: operation 3196
feature list: operation 3672
license: BSD-3-Clause

DeepPoseKit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0610
application sub category: topic 3304
application sub category: topic 3474
application sub category: topic 3500
citation: ELIFE.47994
citation: pmcid:PMC6897514
citation: pubmed:31570119
description: A software toolkit for fast and robust animal pose estimation using deep learning. DeepPoseKit is a software toolkit with a high-level API for 2D pose estimation of user-defined keypoints using deep learning—written in Python and built using Tensorflow and Keras.
feature list: operation_0337
feature list: operation 3215
feature list: operation 3799
license: Apache-2.0

DeepPromise
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3511
application sub category: topic 3512
citation: BBZ112
citation: pubmed:31714956
description: Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. RNA post-transcriptional modifications play a crucial role in a myriad of biological processes and cellular functions. To date, more than 160 RNA modifications have been discovered; therefore, accurate identification of RNA-modification sites is fundamental for a better understanding of RNA-mediated biological functions and mechanisms. However, due to limitations in experimental methods, systematic identification of different types of RNA-modification sites remains a major challenge. Recently, more than 20 computational methods have been developed to identify RNA-modification sites in tandem with high-throughput experimental methods, with most of these capable of predicting only single types of RNA-modification sites
feature list: operation_0278
feature list: operation_0417
feature list: operation_0443
software help: https://deeppromise.erc.monash.edu/center.php

DeepRank
type: SoftwareApplication
input: Protein-ligand complex
  type: FormalParameter
  additional type: data 1461
  encoding format: format 1476
output: Structure similarity score
  type: FormalParameter
  additional type: data_0888
  encoding format: format 3590
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic 2814
citation: https://doi.org/10.1101/2021.01.29.425727
description: DeepRank is a general, configurable deep learning framework for data mining protein-protein interactions (PPIs) using 3D convolutional neural networks (CNNs). DeepRank contains useful APIs for pre-processing PPIs data, computing features and targets, as well as training and testing CNN models.
feature list: operation 2996
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest
software version: 0.2.0

DeepRiPP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 2229
application sub category: topic 3172
application sub category: topic 3314
application sub category: topic 3474
citation: pnas.1901493116
citation: pmcid:PMC6955231
citation: pubmed:31871149
description: DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products. Deepginsen is a lantipeptide that is genomically encoded distantly from its modification enzymes and discovered directly as a result of DeepRiPP within the genome and metabolome of Flavobacterium ginsengiterrae JCM 17337.
feature list: operation_0436
feature list: operation 3629

DeepSV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3175
application sub category: topic 3382
application sub category: topic 3474
citation: S12859-019-3299-Y
citation: pmcid:PMC6909530
citation: pubmed:31830921
description: A accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network. Calling deletions using deep convolutional neural. DeepSV, an approach based on deep learning for calling long deletions from sequence reads.DeepSV is based on a novel method of visualizing sequence reads. The visualization is designed to capture multiple sources of information in the data that are relevant to long deletions. DeepSV also implements techniques for working with noisy training data. DeepSV trains a model from the visualized sequence reads and calls deletions based on this model. We demonstrate that DeepSV outperforms existing methods in terms of accuracy and efficiency of deletion calling on the data from the 1000 Genomes Project. Our work shows that deep learning can potentially lead to effective calling of different types of genetic variations that are complex than SNPs
feature list: operation_0337
feature list: operation_0484
feature list: operation 3199
feature list: operation 3227

DeepScreening
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0632
application sub category: topic 3336
application sub category: topic 3375
application sub category: topic 3474
citation: BAZ104
citation: pmcid:PMC6790966
citation: pubmed:31608949
description: A deep learning-based screening web server for accelerating drug discovery. DeepScreening is a useful platform to help drug researchers do virtual screening conveniently and fast through deep learning. DeepScreening is a user-friendly web server for constructing deep learning models using public dataset or user provided dataset, which would help biologist and chemist virtual screening the chemical probes or drugs for a specific target of interest.
feature list: operation 3644
feature list: operation 3659

DeepSeqPanII
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 2830
application sub category: topic 3474
citation: https://doi.org/10.1101/817502
description: An interpretable recurrent neural network model with attention mechanism for peptide-HLA class II binding prediction. A sequence-based pan model for peptide-MHC II binding affinity prediction.
feature list: operation_0252
feature list: operation_0416
feature list: operation 3439

DeepShape
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0108
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3512
citation: S12859-019-3244-0
citation: pmcid:PMC6923924
citation: pubmed:31861979
description: Estimating isoform-level ribosome abundance and distribution with Ribo-seq data. For the estimation of Isoform-Level Ribosome Abundance and Distribution Accurately which needs Ribo-seq data only.
feature list: operation_0492
feature list: operation 2495
feature list: operation 3800

DeepSide
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0208
application sub category: topic_0209
application sub category: topic 2840
application sub category: topic 3379
citation: https://doi.org/10.1101/843029
description: A Deep Learning Framework for Drug Side Effect Prediction. Drug failures due to unforeseen adverse effects at clinical trials pose health risks for the participants and lead to substantial financial losses
feature list: operation 2495
license: MIT

DeepSpCas9
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0157
application sub category: topic_0749
application sub category: topic 3168
citation: https://doi.org/10.1101/636472
citation: SCIADV.AAX9249
citation: pmcid:PMC6834390
citation: pubmed:31723604
description: A deep learning-based model with unparalleled generalization performance | We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing sgRNA-encoding and target sequence pairs. Deep learning-based training on this large data set of SpCas9-induced indel frequencies led to the development of a SpCas9-activity predicting model named DeepSpCas9. When tested against independently generated data sets (our own and those published by other groups), DeepSpCas9 showed unprecedentedly high generalization performance. DeepSpCas9 is available at http: deepcrispr.info DeepCas9
software help: help

DeepSplice
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3512
citation: s12864-018-5350-1
citation: pmcid:PMC6307148
citation: pubmed:30591034
description: Deep learning based splice junction sequence classifier.
feature list: operation_0264
feature list: operation_0433
feature list: operation_0446
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Yi Zhang

DeepSymNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3360
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3577
citation: FNINS.2019.01053
citation: pmcid:PMC6788344
citation: pubmed:31636533
description: Quantifying Neurodegenerative Progression With DeepSymNet. A data-driven method based that identifies longitudinal changes in 3D structural MRI data without relying on prior brain regions of interest, an atlas, or non-linear registration pipelines.
feature list: operation 3435
feature list: operation 3659

Deep Functional Synthesis (DeepSyn)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0634
application sub category: topic 3068
application sub category: topic 3474
application sub category: topic 3518
citation: https://doi.org/10.1101/824086
description: A machine learning approach to gene functional enrichment. Deep functional synthesis: a machine learning approach to gene function enrichment. Deep Functional Synthesis (DeepSyn) is function annotation tool that moves beyond gene function databases to dynamically infer the functions of a gene set from its associated network of literature and data, conditioned on the disease and drug context of the current experiment.
feature list: operation 2454
feature list: operation 3501
feature list: operation 3672

DeepType
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0091
application sub category: topic 2640
application sub category: topic 3361
citation: https://doi.org/10.1101/629865
description: Deep Learning Approach to Identifying Breast Cancer Subtypes Using High-Dimensional Genomic Data.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Yijun Sun

DeepUbi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0602
citation: s12859-019-2677-9
citation: pmcid:PMC6379983
citation: pubmed:30777029
description: Deep Learning Framework for Prediction of Ubiquitination Sites in Proteins.
feature list: operation_0417
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

Deep Docking
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 2840
application sub category: topic 3047
application sub category: topic 3336
citation: acscentsci.0c00229
citation: https://doi.org/10.1101/2019.12.15.877316
citation: pmcid:PMC7318080
citation: pubmed:32607441
description: A Deep Learning Approach for Virtual Screening of Big Chemical Datasets. Drug discovery is an extensive and rigorous process that requires up to 2 billion dollars of investments and more than ten years of research and development to bring a molecule “from bench to a bedside”. While virtual screening can significantly enhance drug discovery workflow, it ultimately lags the current rate of expansion of chemical databases that already incorporate billions of purchasable compounds. This surge of available small molecules presents great opportunities for drug discovery but also demands for faster virtual screening methods and protocols. In order to address this challenge, we herein introduce Deep Docking ( D 2 ) - a novel deep learning-based approach which is suited for docking billions of molecular structures.
feature list: operation_0478
license: MIT

Deep Splicing Code (DSC)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3320
application sub category: topic 3512
citation: GENES10080587
citation: pmcid:PMC6722613
citation: pubmed:31374967
description: Classifying Alternative Splicing Events Using Deep Learning | Alternative splicing (AS) is the process of combining different parts of the pre-mRNA to produce diverse transcripts and eventually different protein products from a single gene. In computational biology field, researchers try to understand AS behavior and regulation using computational models known as "Splicing Codes". The final goal of these algorithms is to make an in-silico prediction of AS outcome from genomic sequence. Here, we develop a deep learning approach, called Deep Splicing Code (DSC), for categorizing the well-studied classes of AS namely alternatively skipped exons, alternative 5'ss, alternative 3'ss, and constitutively spliced exons based only on the sequence of the exon junctions
feature list: operation_0264
feature list: operation_0433
feature list: operation_0446

DeltaNeTS+
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3512
citation: https://doi.org/10.1101/788968
description: Elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks. DeltaNeTS+ is a major improvement to our previous method DeltaNet. DeltaNeTS+ is a method for inferring direct gene targets of drug compounds and diseases from steady-state and/or time-series transcriptional profiles. DeltaNeTS+ incorporates gene regulatory information (if avaialbe) during the inference. DeltaNeTS+ generates a perturbation score for each gene in every sample. The score magnitude reflects the confidence that the transcription process of this gene was directly affected by the external stimuli. The score sign indicates the nature of the perturbation: positive for gene induction, negative for gene repression
feature list: operation 1781
feature list: operation 2495
feature list: operation 3439
feature list: operation 3766
license: GPL-3.0

Dentareport
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3399
application sub category: topic 3405
citation: J.COMPBIOMED.2019.103437
citation: pubmed:31521901
description: Automated longevity and risk factor analysis in dental patient care | BACKGROUND AND OBJECTIVE:During routine patient care practitioners have to document several aspects. However, currently it is difficult to methodically analyze the longevity of therapeutic concepts in dental private practice. Thus, the aim of the present paper was to introduce a software (Dentareport) to compare the success of different treatment options and to identify risk factors for failures in dental patient care. METHODS:Dentareport has a digital interface to automatically collect data of electronic patient files of practice management programs. By using computer-aided routines descriptive analyses of the treatments can be visualized. Dentareport also visually displays a bivariate risk factor analysis of treatment options

DepMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 2269
application sub category: topic 2640
application sub category: topic 3518
citation: https://doi.org/10.1101/720243
description: Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines | The Cancer Dependency Map Project at Broad Institute | A resource of data and computational tools to expose the vulnerabilities of cancer, and for identifying targets for therapeutic development and designing strategies to optimize patient responses | Explore the Cancer Dependency Map | The goal of the Dependency Map (DepMap) portal is to enable the research community to make discoveries related to cancer vulnerabilities by providing free and timely access to the datasets, visualizations, and analysis tools that are being used by the Cancer Dependency Map Project at the Broad Institute
feature list: operation 3557
feature list: operation 3629
feature list: operation 3891

DepthFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3295
application sub category: topic 3321
application sub category: topic 3518
description: Tool to determine the optimal read depth for reduced-representation sequencing.
feature list: operation_0484
feature list: operation 3196
feature list: operation 3230
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: README.md
primary contact: Jerome Laroche

DesignSignatures
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0632
application sub category: topic 3168
citation: btw047
citation: pubmed:26803162
description: Tool for designing primers that yields amplicons with distinct signatures.
feature list: operation_0308
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Documentation-Manual.html
primary contact: Kalin H. Vetsigian

DetSpace
type: SoftwareApplication
input: Small molecule structure
  type: FormalParameter
  additional type: data 1463
  encoding format: format 2330
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
  encoding format: format 2585
  encoding format: format 3464
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic 3307
application sub category: topic 3895
citation: gkae287
citation: pmcid:PMC11223873
citation: pubmed:38634809
description: A web server for engineering detectable pathways for bio-based chemical production.
feature list: operation 3929
is accessible for free: true
license: MIT
operating system: Linux
software help: detspace
software version: 1.0

Deuteros
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
citation: btz022
citation: pmcid:PMC6736138
citation: pubmed:30649183
description: Software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry.
feature list: operation_0252
feature list: operation 2929
feature list: operation 3631
is accessible for free: true
license: Apache-2.0
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Argyris Politis

DeviaTE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic_0798
application sub category: topic 2885
citation: https://doi.org/10.1111/1755-0998.13030
citation: pmcid:PMC6791034
citation: pubmed:31056858
description: Assembly-free analysis and visualization of mobile genetic element composition.
feature list: operation_0427
feature list: operation 3219
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md

DiNGO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic 3332
citation: BTZ836
citation: pubmed:31702762
description: Standalone application for Gene Ontology and Human Phenotype Ontology term enrichment analysis. DiNGO is a standalone application based on open source code from BiNGO a Java based tool aimed to determine which Gene Ontology (GO) categories are overrepresented in a set of genes. DiNGO is a command line application which is able to do GO and HPO term enrichment on a set of genes or proteins. DiNGO is multithreaded application which offers fast processing of large datasets. In addition, the application offers gene/protein identifiers conversion tool as well as automatic download of HPO and GO annotation resources.
feature list: operation 3431
feature list: operation 3501
license: GPL-3.0
software help: DiNGO Manual.pdf

DiVenn
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic 3170
citation: FGENE.2019.00421
citation: pmcid:PMC6509638
citation: pubmed:31130993
description: Interactive and Integrated Web-Based Visualization Tool for Comparing Gene Lists.
feature list: operation_0277
feature list: operation_0533
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Liang Sun
primary contact: Yinbing Ge
primary contact: Zach Robinson

DiagnoProt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic 3474
application sub category: topic 3520
citation: btx093
citation: pubmed:28186229
description: Tool for discovery of new molecules by mass spectrometry.
feature list: operation 3627
feature list: operation 3645
feature list: operation 3803
is accessible for free: true
license: Unlicense
operating system: Windows
software help: tutorial.html
primary contact: André R.F Silva

DiffAtOnce
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0593
description: Software package able to obtain quantitative self-diffusion data in a very straightforward manner allowing the calculation of radii including different molecular models which is not only restricted to spheres.
is accessible for free: false
license: Proprietary
operating system: Linux
operating system: Mac
operating system: Windows

DiffExpress
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: FGENE.2019.00356
citation: pmcid:PMC6527599
citation: pubmed:31139204
description: Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis.
feature list: operation 3223
feature list: operation 3680
feature list: operation 3800
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Document
software help: Support
primary contact: Cintia C. Palu
primary contact: Paul Walsh

DigChem
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3474
citation: JOURNAL.PCBI.1007022
citation: pmcid:PMC6519793
citation: pubmed:31091224
description: Identification of disease-gene-chemical relationships from Medline abstracts.
feature list: operation 2422
feature list: operation 3280
feature list: operation 3625
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0003-2389-7183

DigestiFlow
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic 2229
citation: PEERJ.PREPRINTS.27717
description: Web-based database system for flow cell management.
feature list: operation 3431
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest
primary contact: Manuel Holtgrewe

Digitaldlsorter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0804
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3474
citation: FGENE.2019.00978
citation: pmcid:PMC6824295
citation: pubmed:31708961
description: Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data. A pipeline to generate a Deep Nerual Network cell type deconvolution model for bulk RNASeq samples from single cell experiment data. A pipeline to generate a Deep Neural Network cell type deconvolution model for bulk RNASeq samples from single cell rna-seq data. The pipeline runs in R 3.51 and python 3.6.8. conda create env -n digitalDLSorter
feature list: operation_0560
feature list: operation 3629
feature list: operation 3800

DisCVR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3174
application sub category: topic 3305
application sub category: topic 3519
citation: VEZ033
citation: pmcid:PMC6735924
citation: pubmed:31528358
description: Rapid viral diagnosis from high-throughput sequencing data | High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance, and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample k-mers (twenty-two nucleotide sequences) to k-mers from taxonomically labeled viral genomes. DisCVR was validated using published HTS data for eighty-nine clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method
feature list: operation 3196
feature list: operation 3472

DisConICA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3360
application sub category: topic 3384
application sub category: topic 3444
citation: s12021-019-09422-1
citation: pmcid:PMC6904532
citation: pubmed:31187352
description: Software Package for Assessing Reproducibility of Brain Networks and their Discriminability across Disorders.
feature list: operation 3432
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: Instructions for Processing with DisConICA 1 01 1.pdf
software help: Instructions for Processing with DisConICA 1 01 2.pdf
software version: 1.01.1
software version: 1.01.2

DisV-HPV16
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0622
application sub category: topic 3170
application sub category: topic 3512
citation: s12879-019-4123-z
citation: pmcid:PMC6542142
citation: pubmed:31142265
description: Software for HPV detection in RNA sequencing data.
feature list: operation 3196
feature list: operation 3359
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac

DiscoRhythm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web application
application sub category: topic_0091
application sub category: topic_0121
application sub category: topic_0769
application sub category: topic 3063
citation: btz834
citation: pmcid:PMC7703757
citation: pubmed:31702788
description: An easy-to-use web application and R package for discovering rhythmicity. An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface. Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. DiscoRhythm is available as a web application or an R/Bioconductor package for estimating phase, amplitude, and statistical significance using four popular approaches to rhythm detection (Cosinor, JTK Cycle, ARSER, and Lomb-Scargle). Informative visualizations, interactive modules for quality control, dimensionality reduction, periodicity profiling, and incorporation of experimental replicates make DiscoRhythm a thorough toolkit for analyzing rhythmicity.
feature list: operation_0337
feature list: operation 3454
feature list: operation 3891
license: GPL-3.0

DiscoverSL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic 2640
citation: bty673
citation: pmcid:PMC6378931
citation: pubmed:30059974
description: R package for multi-omic data driven prediction of synthetic lethality in cancers.
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: DiscoverSL manual.pdf
software version: 1.0

DiscoverY
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0654
application sub category: topic 3336
citation: S12864-019-5996-3
citation: pmcid:PMC6688218
citation: pubmed:31399045
description: A classifier for identifying Y chromosome sequences in male assemblies | BACKGROUND:Although the Y chromosome plays an important role in male sex determination and fertility, it is currently understudied due to its haploid and repetitive nature. Methods to isolate Y-specific contigs from a whole-genome assembly broadly fall into two categories. The first involves retrieving Y-contigs using proportion sharing with a female, but such a strategy is prone to false positives in the absence of a high-quality, complete female reference. A second strategy uses the ratio of depth of coverage from male and female reads to select Y-contigs, but such a method requires high-depth sequencing of a female and cannot utilize existing female references. RESULTS:We develop a k-mer based method called DiscoverY, which combines proportion sharing with female with depth of coverage from male reads to classify contigs as Y-chromosomal
feature list: operation_0452
feature list: operation_0484
feature list: operation_0525
license: MIT

Disentangling sRNA-Seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3512
citation: gkz1198
citation: pmcid:PMC7038986
citation: pubmed:31879784
description: Scripts for disentangling small RNA-sequencing (sRNA-Seq) data for libraries containing information from two interacting organisms to study RNA communication between species.
feature list: operation_0523
feature list: operation_0524
feature list: operation 3258
feature list: operation 3792

DistAA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic_0736
citation: J.COMPBIOLCHEM.2019.107130
citation: pubmed:31593887
description: Database of amino acid distances in proteins and web application for statistical review of distances. Three-dimensional structure of a protein chain is determined by its amino acid interactions. One approach to the analysis of amino acid interactions refers to geometric distances of amino acid pairs in polypeptide chains. For a detailed analysis of the amino acid distances, the database with three types of amino acid distances in a set of chains was created. Web application Distances of Amino Acids has also been developed to enable scientists to explore interactions of amino acids with different properties based on distances stored in the database. Web application calculates and displays descriptive statistics and graphs of amino acid pair distances with selected properties, such as geometric distance threshold, corresponding SCOP class of proteins and secondary structure types.
feature list: operation_0267
feature list: operation_0272
feature list: operation 2488

Divergence
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
application sub category: topic 3174
application sub category: topic 3518
citation: https://doi.org/10.1101/720391
description: An R Package for Divergence Analysis of Omics Data | Given the ever-increasing amount of high-dimensional and complex omics data becoming available, it is increasingly important to discover simple but effective methods of analysis. Divergence analysis transforms each entry of a high-dimensional omics profile into a digitized (binary or ternary) code based on the deviation of the entry from a given baseline population. This is a novel framework that is significantly different from existing omics data analysis methods: it allows digitization of continuous omics data at the univariate or multivariate level, facilitates sample level analysis, and is applicable on many different omics platforms
feature list: operation 2495
feature list: operation 3891
license: GPL-2.0

DiversityAgents
type: SoftwareApplication
input: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
  encoding format: format 2333
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
  encoding format: format 2333
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
  encoding format: format 2332
  encoding format: format 2333
output: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
  encoding format: format 2333
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3070
application sub category: topic 3071
description: DiversityAgents (DWB-DA) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DA is focused on the management of agents, that means persons and organisations. In this context it is designed to manage names (variant names, different names, academic degrees, standardized abbreviations etc.), bibliographic data, postal addresses, agent relation to projects, resources like images and documents and additional agent-related data including agent IDs and the hierarchy of person-related data.
feature list: operation 2409
feature list: operation 3349
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: DWB user manuals
software help: Training materials
primary contact: https://orcid.org/0000-0003-1980-3148

DiversityCollection
type: SoftwareApplication
input: Ecological data
  type: FormalParameter
  additional type: data 3736
  encoding format: format 2330
input: Biodiversity data
  type: FormalParameter
  additional type: data 3707
  encoding format: format 2330
  encoding format: format 2331
  encoding format: format 3706
output: Biodiversity data
  type: FormalParameter
  additional type: data 3707
  encoding format: format 2330
  encoding format: format 2331
  encoding format: format 2332
  encoding format: format 3706
output: Ecological data
  type: FormalParameter
  additional type: data 3736
  encoding format: format 2330
  encoding format: format 2331
  encoding format: format 2332
  encoding format: format 3706
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web service
application sub category: topic_0622
application sub category: topic_0780
application sub category: topic 3050
application sub category: topic 3071
application sub category: topic 3299
application sub category: topic 3301
application sub category: topic 3382
application sub category: topic 3500
application sub category: topic 3678
application sub category: topic 3679
description: DiversityCollection (DWB-DC) is an application of the Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DC is designed for data describing collection events, collections, collection vouchers and specimens, parts of specimens, as well as observation and occurrence data with assigned multimedia objects and documents. It is processing any action concerning the gathering, storage, transaction and treatment of specimens in a collection and is also appropriate to store observation data with analyses added. DC is unique among collection management systems by its focus on biological relations between organisms linked together as one or more specimens or observations (e. g., host, parasite, hyperparasite, symbionts, etc.) and by its interoperability through internal and external services.
feature list: operation_0226
feature list: operation_0337
feature list: operation 2409
feature list: operation 2945
feature list: operation 3429
feature list: operation 3434
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: DWB user manuals
software help: DiversityCollection Information Models
software help: Support
software help: Training materials
primary contact: https://orcid.org/0000-0003-1980-3148

DiversityDescriptions
type: SoftwareApplication
input: Experimental measurement
  type: FormalParameter
  additional type: data 3108
  encoding format: format 2332
  encoding format: format 2350
input: Biodiversity data
  type: FormalParameter
  additional type: data 3707
  encoding format: format 2330
  encoding format: format 2332
  encoding format: format 2350
input: Ecological data
  type: FormalParameter
  additional type: data 3736
  encoding format: format 2330
  encoding format: format 2332
  encoding format: format 2350
output: Biodiversity data
  type: FormalParameter
  additional type: data 3707
  encoding format: format 2331
  encoding format: format 2332
  encoding format: format 2350
output: Experimental measurement
  type: FormalParameter
  additional type: data 3108
  encoding format: format 2332
  encoding format: format 2350
output: Ecological data
  type: FormalParameter
  additional type: data 3736
  encoding format: format 2332
  encoding format: format 2350
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0610
application sub category: topic 3050
application sub category: topic 3070
application sub category: topic 3071
application sub category: topic 3391
application sub category: topic 3678
application sub category: topic 3855
citation: baz002
contributor: Universität Bayreuth, Department of Mycology
description: DiversityDescriptions (DWB-DD) is an application of the Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. DD has a generic database model. It is organising descriptions of organisms, taxa, syntaxa and any item, which is object of diversity research. The descriptions are characterized by a triple structure, namely ’item-descriptor-state’. The states can be generalized to one of the presently supported data types (categorical states, quantitative values and measures, molecular sequence data and free-form text). The descriptors (=properties) are not limited to morphological characters and functional traits, but could be physiological, ecological, behavioral , survey parameters, molecular descriptors, descriptors of a lab workflow, descriptors of data content schemes. Sample data and measurement data as gained by ecological field sampling are addressed with own functions.
feature list: operation 2409
feature list: operation 2429
feature list: operation 2945
feature list: operation 3434
feature list: operation 3438
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: DWB training environment
software help: DWB user manuals
software help: DiversityDescriptions Information Models
primary contact: https://orcid.org/0000-0003-1980-3148

DiversityExsiccatae
type: SoftwareApplication
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
output: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
  encoding format: format 2332
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
  encoding format: format 2332
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Desktop application
additional type: Web service
application sub category: topic 3068
application sub category: topic 3070
application sub category: topic 3071
contributor: SNSB, Botanische Staatssammlung München
description: DiversityExsiccatae (DWB-DE) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DE is currently used in a core installation at the SNSB, Botanische Staatssammlung München to manage bibliographic information and standardized abbreviations of botanical and mycological exsiccatae in a global index. Exsiccatae are series of specimen collections which are distributed as a publication together with assigned printed matters. They are usually available in multiple copies worldwide. This standard list for Exsiccatal series with unique and stable series identifers is increasing the efficiency of the digitization of botanical and mycological collections.
feature list: operation 2409
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: webservice.jsp
software help: DWB user manuals
software help: DiversityExsiccatae Information Models
software help: Training materials
primary contact: https://orcid.org/0000-0003-1980-3148

DiversityGazetteers
type: SoftwareApplication
input: Map
  type: FormalParameter
  additional type: data 1274
  encoding format: format 2333
input: Ontology data
  type: FormalParameter
  additional type: data 2353
  encoding format: format 2330
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
output: Ontology data
  type: FormalParameter
  additional type: data 2353
  encoding format: format 2330
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
output: Map
  type: FormalParameter
  additional type: data 1274
  encoding format: format 2333
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3071
application sub category: topic 3855
description: DiversityGazetteers (DWB-DG) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DG is used to manage and visualize geographical dictionary entries with information about places (particular regions and locations). In conjunction with an automatically created background map, equipped with world coordinates, collections of Microsoft SQL Geometry Objects (points, lines and areas) are displayed in their geographical context. Users with administrator rights may import places from other sources (e. g., ArcView shape files) or create places manually using the integrated Diversity GIS Editor. They may also organise the classification and naming of places.
feature list: operation_0337
feature list: operation 2409
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: DWB user manuals
software help: DiversityGazetteers Information Models
software help: Training materials
primary contact: https://orcid.org/0000-0003-1980-3148

DiversityImageInspector
type: SoftwareApplication
input: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 2333
  encoding format: format 2350
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
output: Text
  type: FormalParameter
  additional type: data 3671
  encoding format: format 2330
output: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3070
application sub category: topic 3071
contributor: Universität Bayreuth, Department of Mycology
description: The DiversityImageInspector (DWB-DII) is a stand-alone application of Diversity Workbench (DWB). It might be installed as an independent tool. The DII is designed to scan a bulk of images for included barcodes and relevant EXIF metadata (e.g., GPS coordinates, date, time) and returns the results in a table. The table can be saved as text file (CSV) along with the corresponding image file names. DII is able to rename the multimedia input files by adding a prefix to the file name to fit, e. g., the naming convention of an image data repository. This feature might be used to organize the multimedia file storage, e. g. on a web server. DII combines the functions of two freeware tools: (a) ExifTool, to extract the search tags from the metadata of an image and (b) ZBar bar code reader, to find barcodes within a picture. The latter software supports barcodes of the following types: EAN-13/UPC-A, UPC-E, EAN-8, Code 128, Code 39, Interleaved 2 of 5 and QR Code.
feature list: operation 2409
feature list: operation 3438
feature list: operation 3443
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center

DiversityMobile
type: SoftwareApplication
input: Biodiversity data
  type: FormalParameter
  additional type: data 3707
  encoding format: format 2330
  encoding format: format 3706
input: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3579
input: Ecological data
  type: FormalParameter
  additional type: data 3736
  encoding format: format 2330
  encoding format: format 3706
output: Biodiversity data
  type: FormalParameter
  additional type: data 3707
  encoding format: format 2330
  encoding format: format 3706
output: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3579
output: Ecological data
  type: FormalParameter
  additional type: data 3736
  encoding format: format 2330
  encoding format: format 3706
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web service
application sub category: topic 3050
application sub category: topic 3070
application sub category: topic 3071
author: University of Bayreuth, Chair of Databases and Information Systems
contributor: Universität Bayreuth, Department of Mycology
description: DiversityMobile (DWB-DM) is an smartphone app for biologists, ecologists and registered citizen scientists being experienced in recording observation data in the field. Data are entered into the app database which follows the Diversity Workbench (DWB) information model. Mechanisms of automated recording and storage of GPS data and manual recording of multimedia data are included. Data entry might be done offline. The DM virtual environment covers webservices for bidirectional data transfer with an institutional data repository. Features include the recording of research data and metadata with automatic inclusion of GPS data, recording of multimedia data (images, audio, video), data transfer from and to an institutional data repository via Wi-Fi. DM webservices are ready to download standardised pick lists with names of organisms, geographic maps and already available metadata of individual research projects. DM webservices are also used to upload research data to the data repository.
feature list: operation 2409
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
software help: DiversityMobile User Manuals WP
software help: DiversityMobile
primary contact: SNSB IT Center

DiversityProjects
type: SoftwareApplication
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
  encoding format: format 2332
input: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
  encoding format: format 2332
output: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
  encoding format: format 2332
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
  encoding format: format 2332
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web service
application sub category: topic 3070
application sub category: topic 3071
application sub category: topic 3678
description: DiversityProjects (DWB-DP) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DP is focused on the management of (research) projects, data collections, processed by the other DWB modules. It is managing metadata , labels, descriptors, and descriptions of projects, including data package-specific settings for a metadata standard-compliant publication. DP is organising the storage of (legal) documents, permits, information on publications and multimedia resources. DP is handling roles of persons and organisations involved in collection and research projects. The tool is organising project classification and hierarchy in relation to sister and umbrella projects as well as the storage of each type of stable identifier related to data packages. DP is managing issues on web presentation of data collections.
feature list: operation 2409
feature list: operation 2428
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: DWB user manuals
software help: Training materials
primary contact: https://orcid.org/0000-0003-1980-3148

DiversityReferences
type: SoftwareApplication
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
  encoding format: format 2332
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
  encoding format: format 2332
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3068
application sub category: topic 3070
application sub category: topic 3071
description: DiversityReferences (DWB-DR) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DR is focussed on the management of bibliographic data about each kind of scientific publications. The tool is handling literature annotations, abstracts, keywords and any kind of descriptors and publication object identifiers. DR is able to import and export literature citations and is used to organise documents and multimedia resources.
feature list: operation_0226
feature list: operation 2409
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: DWB user manuals
software help: DiversityReferences Information Models
software help: Training materials

DiversitySamplingPlots
type: SoftwareApplication
input: Ecological data
  type: FormalParameter
  additional type: data 3736
  encoding format: format 2330
  encoding format: format 2333
output: Ecological data
  type: FormalParameter
  additional type: data 3736
  encoding format: format 2330
  encoding format: format 2333
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3071
application sub category: topic 3855
description: DiversitySamplingPlots (DWB-DSP) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DSP is focussed on the management of sampling plots. It is a tool designed for biodiversity, geodiversity, ecological and geosciences research projects. In this context it is appropriate to design plots, organise the geographical position of geoobjects and the geometry of the plots as well as of georeferenced objects found on the plots. DSP is able to import sampling plots from other sources and formats (e. g., ArcView shape files) classifying them hierarchically and annotating them. The Diversity GIS Editor is integrated.
feature list: operation 2409
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: DWB user manuals
software help: DiversitySamplingPlots Information Models
software help: Training materials
primary contact: https://orcid.org/0000-0003-1980-3148

DiversityScientificTerms
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
  encoding format: format 2330
  encoding format: format 2332
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
  encoding format: format 2332
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
  encoding format: format 2332
output: Ontology data
  type: FormalParameter
  additional type: data 2353
  encoding format: format 2330
  encoding format: format 2332
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0089
application sub category: topic 3070
application sub category: topic 3071
application sub category: topic 3303
application sub category: topic 3314
application sub category: topic 3855
description: DiversityScientificTerms (DWB-DST) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DST is focussed on the management of collections of scientific terms and term concepts, i. e., particular domain-specific terminologies, glossaries and vocabularies (e.g. biostratigraphy, anatomical terminology). DST is able to organise terms together with synonyms, common names and equivalent terms ín different languages. The single terms are defined, (hierarchically) classified and referenced, for example, by linking online resources and external identifiers.
feature list: operation 2409
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: DWB user manuals
software help: DiversityScientificTerms Information Models
software help: Training materials
primary contact: https://orcid.org/0000-0003-1980-3148

DiversityTaxonNames
type: SoftwareApplication
input: Taxonomy
  type: FormalParameter
  additional type: data 3028
  encoding format: format 2330
  encoding format: format 2332
output: Taxonomy
  type: FormalParameter
  additional type: data 3028
  encoding format: format 2330
  encoding format: format 2332
  encoding format: format 2376
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web API
additional type: Web service
application sub category: topic_0089
application sub category: topic 3070
application sub category: topic 3071
description: DiversityTaxonNames (DWB-DTN) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DTN is focused on the management of taxon names. Next to nomenclatural information on zoological, botanical, mycological, palaeontological, bacteriological taxon names like typification with type specimens, homotypic synonyms, basionyms, protologues and references according to the rules of the respective International Codes, it is designed to document taxonomic information. This includes accepted names (current names), heterotypic synonyms, name concepts and classifications as well as the history of changing taxonomic relations. DTN is also used to organise common names in various languages and regional taxon checklists with information on red list status and other taxon-based (ecological and nature conservation) parameters.
feature list: operation 2409
feature list: operation 2945
feature list: operation 2990
feature list: operation 3434
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: DWB user manuals
software help: DiversityTaxonNames Information Models
software help: Training materials
primary contact: https://orcid.org/0000-0003-1980-3148

Diversity GIS Editor
type: SoftwareApplication
input: Map
  type: FormalParameter
  additional type: data 1274
  encoding format: format 2330
  encoding format: format 2333
  encoding format: format 2350
output: Map
  type: FormalParameter
  additional type: data 1274
  encoding format: format 2330
  encoding format: format 2333
  encoding format: format 2350
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0092
application sub category: topic 3071
application sub category: topic 3855
description: The Diversity GIS Editor (DWB-DGE) is a stand-alone application of Diversity Workbench (DWB). It might be installed as an independent module of a DWB environment. Beside this, the DGE is an integrated part of DiversityCollection, DiversityGazetteers and DiversitySamplingPlots. The DGE allows for creating, visualizing, editing and storing samples within a geographical environment. In combination with a background map with world coordinates, collections of Microsoft SQL Geometry Objects (points, lines, areas) may be displayed and edited. The screen and world coordinates of the objects are calculated. Color, thickness and transparency of the elements can be designed. The working area may be shifted or zoomed. The background map could either be loaded from a storage device or created with an online map server tool. Maps without world coordinates may be adjusted to a background map with coordinates by setting reference points. This function allows the georeferencing of historical maps.
feature list: operation_0337
feature list: operation 2409
feature list: operation 2430
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: DWB user manuals
software help: Training materials
primary contact: https://orcid.org/0000-0003-1980-3148

Diversity Workbench
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic_0089
application sub category: topic 3068
application sub category: topic 3070
application sub category: topic 3071
application sub category: topic 3391
application sub category: topic 3678
application sub category: topic 3855
contributor: Universität Bayreuth, Department of Mycology
description: The modularized Diversity Workbench (=DWB) represents a tool suite for the management of life and environmental sciences data. The DWB is handling different kinds of bio- and geodiversity data, taxonomies, terminologies, and facilitates the processing of ecological, molecular biological, observational, collection and taxonomic data. It is capable and flexible enough to be applied as data storage system for institutional data repositories. The DWB is set up on a system of 11 xml-enabled SQL relational databases. The rich clients are installed as desktop applications. The DWB might be run as an intranet solution and provide direct interoperability with clients of interlinked DWB databases including cloud services. DWB installations are flexible in the management of highly structured data, enable sophisticated user administration and allow for user-adapted data entry and data exchange. Further, the DWB design facilitates the dynamic integration of web services and external data resources.
feature list: operation_0226
feature list: operation 2409
feature list: operation 2425
feature list: operation 2945
feature list: operation 3429
feature list: operation 3434
funder: Deutsche Forschungsgemeinschaft (DFG)
is accessible for free: true
license: GPL-2.0
operating system: Windows
provider: SNSB IT Center
software help: About the Diversity Workbench (DWB)
software help: DWB user manuals
software help: Training materials
software help: tools
primary contact: https://orcid.org/0000-0003-1980-3148

Dizzy-Beats
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2259
application sub category: topic 3068
citation: btv062
citation: pmcid:PMC4443683
citation: pubmed:25637558
description: Bayesian evidence analysis tool for systems biology.
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: Home
primary contact: Stuart Aitken

Dmipy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0102
application sub category: topic 3068
application sub category: topic 3306
application sub category: topic 3384
application sub category: topic 3444
citation: FNINF.2019.00064
citation: pmcid:PMC6803556
citation: pubmed:31680924
description: Diffusion MRI Multi-Compartment Modeling and Microstructure Recovery Made Easy. An open source toolbox for reproducible diffusion MRI-based microstructure estimation. Dmipy: Diffusion Microstructure Imaging in Python. The Dmipy software package facilitates the reproducible estimation of diffusion MRI-based microstructure features. It does this by taking a completely modular approach to Microstructure Imaging. Using Dmipy you can design, fit, and recover the parameters of any multi-compartment microstructure model in usually less than 10 lines of code. Created models can be used to simulate and fit data for any PGSE-based dMRI acquisition, including single shell, multi-shell, multi-diffusion time and multi-TE acquisition schemes. Dmipy's main features include:
feature list: operation 2425
feature list: operation 2426
feature list: operation 3629
license: MIT

DoGNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0611
application sub category: topic 3385
application sub category: topic 3474
citation: JOURNAL.PCBI.1007012
citation: pmcid:PMC6533009
citation: pubmed:31083649
description: Deep architecture for synapse detection in multiplexed fluorescence images.
feature list: operation 3216
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0002-4264-8572

Doc2Hpo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic_0625
citation: GKZ386
citation: pmcid:PMC6602487
citation: pubmed:31106327
description: Web application for efficient and accurate Human Phenotype Ontology (HPO) concept curation.
feature list: operation 1812
feature list: operation 3280
feature list: operation 3559
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: faq.jsp
software help: tutorial.jsp
primary contact: https://orcid.org/0000-0002-9624-0214
primary contact: Kai Wang

DockBox
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 3336
citation: S10822-019-00227-7
citation: pubmed:31578656
description: Assessing and improving the performance of consensus docking strategies using the DockBox package. Platform package to simplify the use of docking programs and consensus methods. DockBox is a python wrapper library designed to facilitate the use of standard docking programs either alone or in combination. In addition, DockBox enables to rescore the generated docking poses with different popular scoring algorithms as well as to analyze the results using different consensus docking/scoring strategies
feature list: operation_0482
feature list: operation 3659
feature list: operation 3899

DockThor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic 2275
citation: j.ins.2014.08.002
description: Web Services for Molecular Docking Simulations | A Free Web Server for Protein-ligand Docking | Add missing hydrogen atoms, complete side chains, change protonation states. Simple and easy!
feature list: operation_0249
feature list: operation_0482
feature list: operation 3899

Docker4Circ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic 3053
citation: IJMS21010293
citation: pmcid:PMC6982331
citation: pubmed:31906249
description: It is a new work-flow designed for a comprehensive analysis of circRNAs composed of: the circRNAs prediction, their classification and annotation using public databases, the back-splicing sequence reconstruction, the internal alternative structure definition, the alignment-free circRNAs quantification from RNA-Seq reads, and their differential expression analysis. Docker4Circ was specifically designed for making easier and more accessible circRNA analysis thanks to its containerization and an available user-friendly Java GUI Interface. Furthermore, Docker4Circ ensures a reproducible analysis because all its tasks were embedded into an docker image following guideline provided by Reproducible Bioinformatics Project (RBP, http://reproducible-bioinformatics.org/).
is accessible for free: true
license: GPL-3.0
operating system: Linux
software version: version 1

Domainoid
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0084
application sub category: topic_0130
application sub category: topic_0736
citation: S12859-019-3137-2
citation: pmcid:PMC6816169
citation: pubmed:31660857
description: domain-oriented orthology inference. BACKGROUND:Orthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for its function, and recombination events mean individual domains can have different evolutionary histories. It has previously been shown that orthologous proteins may differ in domain architecture, creating challenges for orthology inference methods operating on full-length sequences. We have developed Domainoid, a new tool aiming to overcome these challenges faced by full-length orthology methods by inferring orthology on the domain level. It employs the InParanoid algorithm on single domains separately, to infer groups of orthologous domains. RESULTS:This domain-oriented approach allows detection of discordant domain orthologs, cases where different domains on the same protein have different evolutionary histories
feature list: operation_0303
feature list: operation_0327
feature list: operation 3435
feature list: operation 3767

Dominance Sharing Assessment
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3474
application sub category: topic 3500
application sub category: topic 3679
citation: J.JTBI.2019.110101
citation: pubmed:31816295
description: Dominance, Sharing, and Assessment in an Iterated Hawk-Dove Game. Animals use a wide variety of strategies to reduce or avoid aggression in conflicts over resources. These strategies range from sharing resources without outward signs of conflict to the development of dominance hierarchies, in which initial fighting is followed by the submission of subordinates. Although models have been developed to analyze specific strategies for resolving conflicts over resources, little work has focused on trying to understand why particular strategies are more likely to arise in certain situations. In this paper, we use a model based on an iterated Hawk-Dove game to analyze how resource holding potentials (RHPs) and other factors affect whether sharing, dominance relationships, or other behaviours are evolutionarily stable
feature list: operation 2426

DoubletDetection
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3475
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3308
application sub category: topic 3572
description: Detection of doublets (technical errors) in single-cell RNA-seq count matrices.
feature list: operation_0337
feature list: operation 3218
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: PBMC 8k vignette.ipynb

DrDiff
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0593
application sub category: topic 3318
application sub category: topic 3892
citation: https://doi.org/10.1063/1.5113499
citation: pubmed:31542001
description: Drift-diffusion (DrDiff) framework determines kinetics and thermodynamics of two-state folding trajectory and tunes diffusion models | Stochastic drift-diffusion (DrDiff) framework can evaluate free energy, drift and diffusion coefficients, transition path and first passage times using trajectory time traces | Drift-diffusion (DrDiff) framework
feature list: operation_0244
license: GPL-3.0

DrLLPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic_0621
application sub category: topic 2229
application sub category: topic 3512
citation: gkz1027
citation: pmcid:PMC7145660
citation: pubmed:31691822
description: A data resource of liquid-liquid phase separation in eukaryotes. Here, we presented a data resource of LLPS (DrLLPS), a comprehensive data resource that contained 437,887 known and computationally detected LLPS-associated proteins in 164 eukaryotic species. Phase separation, or liquid-liquid phase separation (LLPS), is a ubiquitous and important mechanism for the formation of membraneless condensates in cells
feature list: operation 2421
feature list: operation 3216
feature list: operation 3454
software help: guide.php

DrawGlycan-SNFG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0154
application sub category: topic 3520
citation: btz819
citation: pmcid:PMC10251767
citation: pubmed:31710658
description: Rendering glycans and annotating glycopeptide mass spectra. Render glycans and glycopeptides with fragmentation info. using the Symbolic Nomenclature for Glycans [SNFG]. Virtual Glycome Release notes FAQ. IUPAC-condensed Input (glycan or glycopeptide):. If you use this software, please cite: Cheng, K. et al., 'DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information', Glycobiology 27(3): 200-205, 2017 ( Abstract & Full Text )
feature list: operation_0337
feature list: operation 3646
feature list: operation 3755
license: GPL-3.0
software help: DrawGlycanSNFG2 Manual.pdf

DriverDBv4
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0091
application sub category: topic_0199
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3173
citation: gkad1060
citation: pmcid:PMC10767848
citation: pubmed:37956338
description: DriverDBv4 is a cancer omics database which incorporates somatic mutation, RNA expression, miRNA expression, methylation, copy number variation and clinical data in addition to annotation bases.
feature list: operation_0337
feature list: operation 2495
feature list: operation 3207
is accessible for free: true

DriverSub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3518
application sub category: topic 3577
citation: BTZ793
citation: pubmed:31626284
description: Inferring subgroup specific driver genes from heterogeneous cancer samples via subspace learning with subgroup indication. Developer: Jianing Xi xjn@nwpu.edu.cn. Instructions to DriverSub (version 1.0.0). After the raw data are loaded, the script ./GenerateInputData.m with function ./bin/P02_GenerateMutData.m can generate the mutation matrix of BRCA and BLCA as ./InputData/D01_brca.mat and ./InputData/D02_blca.mat. The two generated .mat files are the input data of DriverSub
feature list: operation 2454
feature list: operation 3435
feature list: operation 3439

DrugComb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0605
application sub category: topic 3336
application sub category: topic 3375
citation: GKZ337
citation: gkab438
citation: pmcid:PMC6602441
citation: pmcid:PMC8218202
citation: pubmed:31066443
citation: pubmed:34060634
description: The data portal for drug combination and monotherapy sensitivity screenings. [v1.5] DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal. https://doi.org/10.1093/nar/gkab438 [v1.4] DrugComb: an integrative cancer drug combination data portal. https://doi.org/10.1093/nar/gkz337
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: drugcomb
software version: 1.5
primary contact: https://orcid.org/0000-0001-7480-7710

DrugCombDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic 2640
application sub category: topic 3336
application sub category: topic 3375
citation: gkz1007
citation: pmcid:PMC7145671
citation: pubmed:31665429
description: DrugCombDB is a comprehensive database dedicated to integrating drug combinations from various data sources, include 1) high-throughput screening assays of drug combinations, 2) external databases, and 3) manual curations from PubMed literature.
feature list: operation 2421
feature list: operation 3659
feature list: operation 3799
software help: tutorial

DrugR+
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0154
application sub category: topic 3336
application sub category: topic 3373
citation: J.COMPBIOMED.2019.05.006
citation: pubmed:31096089
description: Database for drug repurposing, combination therapy, and replacement therapy.
feature list: operation_0224
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: faq.html
software help: help.html
primary contact: Ali Masoudi-Nejad
primary contact: Massoud Amanlou
primary contact: Yadollah Omidi
primary contact: Yosef Masoudi-Sobhanzadeh

Drug ReposER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic 3379
citation: GKZ391
citation: pmcid:PMC6602481
citation: pubmed:31106379
description: Web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning.
feature list: operation_0420
feature list: operation_0478
feature list: operation_0480
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: about.html
primary contact: https://orcid.org/0000-0003-4275-4663

Drug Targets
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic 3374
citation: BTZ600
citation: pubmed:31368482
description: A database protal for drug target predictions based knowledge graph embeddings.
feature list: operation_0463
feature list: operation 2489
license: CC-BY-NC-SA-3.0

DstarM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3304
citation: s13428-019-01249-7
citation: pmcid:PMC7148288
citation: pubmed:31062193
description: > MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | > CORRECT NAME OF TOOL COULD ALSO BE 'nondecision', 'DM', 'two-choice' | an R package for analyzing two-choice reaction time data with the D∗M method | The decision process in choice reaction time data is traditionally described in detail with diffusion models. However, the total reaction time is assumed to consist of the sum of a decision time (as modeled by the diffusion process) and the time devoted to nondecision processes (e.g., perceptual and motor processes). It has become standard practice to assume that the nondecision time is uniformly distributed. However, a misspecification of the nondecision time distribution introduces bias in the parameter estimates for the decision model. Recently, a new method has been proposed (called the D∗M method) that allows the estimation of the decision model parameters, while leaving the nondecision time distribution unspecified
feature list: operation 3629
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: DstarM.pdf
primary contact: Don van den Bergh

Dsuite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Suite
application sub category: topic_0084
application sub category: topic_0194
application sub category: topic 2885
citation: https://doi.org/10.1101/634477
description: Fast calculation of the ABBA-BABA statistics across many populations/species.
feature list: operation 3196
feature list: operation 3216
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: analysis of introgression with snp data
primary contact: Milan Malinsky

DupGen_finder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0194
application sub category: topic_0780
application sub category: topic 3810
citation: s13059-019-1650-2
citation: pmcid:PMC6383267
citation: pubmed:30791939
description: Tool for identification of different modes of duplicated gene pairs.
feature list: operation 3501
is accessible for free: true
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Xin Qiao

Dwarna
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3337
author: https://orcid.org/0000-0001-5452-5548
description: Dwarna ('about us' in Maltese) is a blockchain-based dynamic consent application for biobanking. The application, which is served through a WordPress plugin, uses a Hyperledger Fabric blockchain, through Hyperledger Composer, to store research participants' consent changes. In this way, the blockchain stores an immutable consent trail. The application contains functionality to manage research studies, research participants and researchers in WordPress.
is accessible for free: true
license: GPL-3.0
software help: dwarna

DyNeuSR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3304
application sub category: topic 3384
application sub category: topic 3444
citation: NETN A 00093
citation: pmcid:PMC6663215
citation: pubmed:31410378
description: Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis | Geniesse, C., Sporns, O., Petri, G., Saggar, M. (in-press) Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis. Network Neuroscience
feature list: operation 3891
license: BSD-3-Clause

DynOVis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic 3173
citation: S12859-019-2995-Y
citation: pmcid:PMC6693283
citation: pubmed:31409281
description: A web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks | BACKGROUND:The development of high throughput sequencing techniques provides us with the possibilities to obtain large data sets, which capture the effect of dynamic perturbations on cellular processes. However, because of the dynamic nature of these processes, the analysis of the results is challenging. Therefore, there is a great need for bioinformatics tools that address this problem. RESULTS:Here we present DynOVis, a network visualization tool that can capture dynamic dose-over-time effects in biological networks. DynOVis is an integrated work frame of R packages and JavaScript libraries and offers a force-directed graph network style, involving multiple network analysis methods such as degree threshold, but more importantly, it allows for node expression animations as well as a frame-by-frame view of the dynamic exposure
feature list: operation_0277
feature list: operation 3439

DynaStI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0153
application sub category: topic 3172
application sub category: topic 3343
citation: METABO9050085
citation: pmcid:PMC6572260
citation: pubmed:31052310
description: Dynamic Retention Time Database for Steroidomics.
feature list: operation 3454
feature list: operation 3633
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
primary contact: https://orcid.org/0000-0003-3669-6313

Dynalogo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3518
citation: BTZ766
citation: pubmed:31609429
description: Interactive sequence logo with dynamic thresholding of matched quantitative proteomic data. Dynalogo can be run with the following code from within RStudio or deployed on a shiny server. To ensure compatibility, the user can download the current list of packages and Version numbers from the Dynalogo webite by clicking on the "Version Info" text at the top of the application located at https://dynalogo.cam.uchc.edu. Dynalogo: Dynamic Sequence Logos. Dynalogo is a web application which can be used to visualize and explore binding array (ie. peptide array) datasets. It was created to allow the dynamic visualizations of sequence logos for better insight into the relationship between affinity and specificity of binding domains. Please import your dataset or dowlnoad the sample dataset
feature list: operation_0337
feature list: operation 3695
feature list: operation 3799
license: GPL-3.0

Dynamic Meta-Storms
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0637
application sub category: topic 3174
application sub category: topic 3293
application sub category: topic 3697
citation: BTZ910
citation: pubmed:31793979
description: Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level. Dynamic Meta-Storms calculates comprehensive taxonomic and phylogenetic distances/dissimilarities of shotgun metagenomes at the species level. Dynamic Meta-Storms calculates comprehensive taxonomic and phylogenetic distances dissimilarities of shotgun metagenomes at the species level.
feature list: operation 3731
license: GPL-3.0

Dysdera silvatica genome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0196
application sub category: topic_0749
application sub category: topic 3170
citation: GIZ099
citation: pmcid:PMC6701490
citation: pubmed:31430368
description: Scripts used during the genome assembly of Dysdera silvatica.
feature list: operation 3192
feature list: operation 3216
feature list: operation 3501
license: MIT

E-Flow
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0114
application sub category: topic_0121
application sub category: topic_0749
application sub category: topic 2229
application sub category: topic 3308
citation: https://doi.org/10.1101/793976
citation: journal.pone.0240233
citation: pmcid:PMC7549788
citation: pubmed:33045012
description: Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria. vngFCM is a package designed to analyse fluocytometry data of small bacterial cells. Fluocytometer analysis of bacterial cells. install.packages("/path/to/E-Flow", repos=NULL, type="source"). This package has been designed to process FCM data by removing non viable cells, subtracting autofluorescence and reduce the effect of electronic noise coming from the cytometer. It has been designed for the analysis of bacterial cells, where the small dimensions and the low expression pose challanges in the correct interpretation of the data.
feature list: operation 2495
feature list: operation 3435
feature list: operation 3799

E-SNPs and GO
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
input: Sequence variations
  type: FormalParameter
  additional type: data 3498
  encoding format: format 2330
output: Score
  type: FormalParameter
  additional type: data 1772
  encoding format: format 2331
  encoding format: format 3464
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3120
author: https://orcid.org/0000-0002-7359-0633
author: Matteo Manfredi
citation: btac678
citation: pmcid:PMC9710551
citation: pubmed:36227117
description: E-SNPs&GO is a machine-learning method the pathogenicity of human variations. E-SNPs&GO classify input variations into pathogenic or benign.
feature list: operation_0331
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
provider: ELIXIR-ITA-BOLOGNA
software help: help
primary contact: https://orcid.org/0000-0002-0274-5669
primary contact: https://orcid.org/0000-0002-7359-0633
primary contact: Matteo Manfredi

Efficient and Adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: EAGS is a smoothing approach for spatial transcriptome data with ultrahigh resolution. Through the principal component information of the profiling of gene expression and the personally identifiable information between cells, it uses a two-factor adaptive smoothing weight mechanism to determine the neighborhood relationship of cells. Then it uses the self-developed smoothing weight formula to calculate the smoothing contribution and recalculate the gene expression of each cell.

EAT-Rice
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0749
application sub category: topic 3474
application sub category: topic 3512
citation: JOURNAL.PCBI.1006942
citation: pmcid:PMC6505892
citation: pubmed:31067213
description: Predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches.
feature list: operation_0441
feature list: operation 3192
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: about.html
software help: manual.html
primary contact: https://orcid.org/0000-0002-5525-4011

EBIC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3068
application sub category: topic 3295
application sub category: topic 3474
citation: btz027
citation: pmcid:PMC6736067
citation: pubmed:30649199
description: Evolutionary-based BIClustering (EBIC), a next-generation biclustering algorithm for mining genetic data.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: ebic
primary contact: Jason H. Moore
primary contact: Patryk Orzechowski

ECLAIR
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3475
output: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3508
output: Clustered expression profiles
  type: FormalParameter
  additional type: data 3768
  encoding format: format 3033
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3308
citation: gkw452
citation: pmcid:PMC5001598
citation: pubmed:27207878
description: A computational method for the statistical inference of cell lineage relationships from single-cell gene expression data.
feature list: operation_0313
feature list: operation_0571
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

ECMarker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3474
citation: btaa935
citation: https://doi.org/10.1101/825414
citation: pmcid:PMC8150141
citation: pubmed:33305308
description: Interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages. Abstract Gene expression and regulation, a key molecular mechanism driving human disease development, remains elusive, especially at early stages. The increasing amount of genomics data gathered from patients allows for better understanding of gene regulatory mechanisms that occur during disease development at a system level. However, integrating such a large amount of population data is still a challenging task. To address this, we developed an interpretable machine learning model, ECMarker, to predict gene expression biomarkers and regulatory networks specific for disease stages such as early cancer. In particular, ECMarker was built on the semi-restricted Boltzmann machine, a machine learning model with multiple hierarchical layers.
feature list: operation 2436
feature list: operation 2454
feature list: operation 3439

ECOTOOL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2269
application sub category: topic 3068
citation: JOURNAL.PONE.0221238
citation: pmcid:PMC6822939
citation: pubmed:31671102
description: A new toolbox for time series analysis and forecasting. Some Features found in a few packages or none at all.
feature list: operation_0337
feature list: operation 3565
feature list: operation 3659
license: GPL-3.0

EDCluster
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0194
application sub category: topic 2269
application sub category: topic 3293
citation: msaa145
citation: https://doi.org/10.1101/794263
citation: pmcid:PMC7743758
citation: pubmed:32877529
description: EDCluster is a method for obtaining stationary distributions that can be used to construct empirical stationary distribution mixture models.
feature list: operation 3432
feature list: operation 3435
feature list: operation 3891
license: GPL-3.0

The Extensive de novo TE Annotator (EDTA)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic_0749
application sub category: topic_0769
application sub category: topic_0780
application sub category: topic_0798
citation: S13059-019-1905-Y
citation: pmcid:PMC6913007
citation: pubmed:31843001
description: The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.
feature list: operation_0362
feature list: operation_0524
feature list: operation 3629

Open-Electroencephalography (EEG)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
citation: s19040772
citation: pmcid:PMC6413114
citation: pubmed:30781869
description: Platform to enable EEG measurements and general purposes Brain Computer Interface experimentations.

EEGMIR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3334
description: Prototype neurofeedback application.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Windows
primary contact: Jim Peters

EEGSourceSim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3334
citation: J.JNEUMETH.2019.108377
citation: pmcid:PMC6815881
citation: pubmed:31381946
description: A framework for realistic simulation of EEG scalp data using MRI-based forward models and biologically plausible signals and noise | BACKGROUND:Electroencephalography (EEG) is widely used to investigate human brain function. Simulation studies are essential for assessing the validity of EEG analysis methods and the interpretability of results. NEW METHOD:Here we present a simulation environment for generating EEG data by embedding biologically plausible signal and noise into MRI-based forward models that incorporate individual-subject variability in structure and function. RESULTS:The package includes pipelines for the evaluation and validation of EEG analysis tools for source estimation, functional connectivity, and spatial filtering. EEG dynamics can be simulated using realistic noise and signal models with user specifiable signal-to-noise ratio (SNR). License either MIT or GLP-2.0

EFI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
additional type: Web application
application sub category: topic_0602
application sub category: topic_0821
application sub category: topic 3174
citation: acs.biochem.9b00735
citation: pmcid:PMC7057060
citation: pubmed:31553576
description: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways | Enzyme Function Initiative Tools | This website contains a collection of webtools for creating and interacting with sequence similarity networks (SSNs) and genome neighborhood networks (GNNs). These tools originated in the Enzyme Function Initiative, a NIH-funded research project to develop a sequence / structure-based strategy for facilitating discovery of in vitro enzymatic and in vivo metabolic / physiological functions of unknown enzymes discovered in genome projects | The Enzyme Function Initiative tools are hosted at the Carl R | If you use the EFI web tools, please cite us: | A "From The Bench" article was recently published in Biochemistry and is available on the training resources page
feature list: operation_0362

EK-DRD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic 3336
application sub category: topic 3379
citation: ACS.JCIM.9B00365
citation: pubmed:31433187
description: A Comprehensive Database for Drug Repositioning Inspired by Experimental Knowledge | Drug Repositioning Drug repositioning, or the identification of new indications for approved therapeutic drugs, has gained substantial traction with both academics and pharmaceutical companies because it reduces the cost and duration of the drug development pipeline and the likelihood of unforeseen adverse events. To date there has not been a systematic effort to identify such opportunities, in part because of the lack of a comprehensive resource for an enormous amount of unsystematic drug repositioning information to support scientists who could benefit from this endeavor | Experimental Knowledge-Based Drug Repositioning Database (EK-DRD) provides a versatile resource for the display, search and analysis of structure, function, pathway, disease, network and related experimentally-validated drug repositioning annotation for 1861 FDA-approved and 102 withdrawn small molecule drugs
feature list: operation_0224
feature list: operation 3454

ELASPIC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Ensemble Learning Approach for Stability Prediction of Interface and Core mutations.
feature list: operation_0250
feature list: operation_0331
feature list: operation 2480
software help: master

ELIMU-MDx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0607
application sub category: topic 3324
application sub category: topic 3489
application sub category: topic 3519
application sub category: topic 3577
citation: BTN-2019-0064
citation: pubmed:31588775
description: The Electronic Laboratory Information and Management Utensil for Molecular Diagnostics (ELIMU-MDx) is a web-based, open-source platform for storage, management and analysis of diagnostic qPCR data. A webapplication for managing, documenting and result analyzing of aPCR Data.
feature list: operation_0337
feature list: operation 3435
feature list: operation 3799
license: MIT

EM-DAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0610
application sub category: topic 3305
application sub category: topic 3489
application sub category: topic 3810
citation: https://doi.org/10.1101/19012633
description: A cross-sectional analysis of the emergency events database from a pediatric perspective. The international disasters database. Disaster group: Two main groups of disasters are distinguished in EM-DAT: natural disasters and technological disasters. This field is automatically linked to the disaster sub-group and the disaster type. There is a third group ‘Complex disasters’ which include some major famine situation for which the drought were not the main causal factor. See Table 1 for the Disasters Classification. In 1988, the Centre for Research on the Epidemiology of Disasters (CRED) launched the Emergency Events Database (EM-DAT).
feature list: operation 3557

EMBL2checklists
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0780
application sub category: topic 3174
application sub category: topic 3512
citation: journal.pone.0210347
citation: pmcid:PMC6328100
citation: pubmed:30629718
description: Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA. Converts EMBL- or GenBank-formatted flat files to submission-ready checklists for submission to ENA via the interactive Webin submission system.
feature list: operation 3192
feature list: operation 3200
feature list: operation 3431
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Michael Gruenstaeudl

EMULSION
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3305
application sub category: topic 3324
application sub category: topic 3474
citation: JOURNAL.PCBI.1007342
citation: pmcid:PMC6760811
citation: pubmed:31518349
description: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology | EMULSION Manual — EMULSION (Epidemiological Multi-Level Simulation framework) | Framework EMULSION is intended for modellers in epidemiology, to help them design, simulate, and revise complex mechanistic stochastic models, without having to write or rewrite huge amounts of code
license: Apache-2.0
software help: Install.html

ENdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0219
application sub category: topic_0749
application sub category: topic 2885
application sub category: topic 3512
citation: GKZ973
citation: pmcid:PMC7145688
citation: pubmed:31665430
description: A manually curated database of experimentally supported enhancers for human and mouse. Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons
feature list: operation_0224
feature list: operation_0440
feature list: operation 2495

EPA-ng
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
application sub category: topic 3293
application sub category: topic 3697
citation: syy054
citation: pmcid:PMC6368480
citation: pubmed:30165689
description: Complete reimplementation of the evolutionary placement algorithm (EPA) that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA and PPLACER.
feature list: operation_0310
feature list: operation_0362
feature list: operation 2495
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
primary contact: Pierre Barbera

EPEE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3170
citation: BTZ398
citation: pubmed:31099391
description: Effector and Perturbation Estimation Engine (EPEE) conducts differential analysis of transcription factor activity from gene expression data.
feature list: operation 2436
feature list: operation 3223
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Murat Can Çobanoğlu

EPI-peptide designer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0154
application sub category: topic 2830
application sub category: topic 3375
citation: btw014
description: Tool for designing peptide ligand libraries based on epitope–paratope interactions.
feature list: operation_0252
feature list: operation_0272
feature list: operation_0416
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: ViartEtAl2015 AllSoftware.zip
primary contact: Viart Benjamin

EPIC-TABSAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3173
application sub category: topic 3518
application sub category: topic 3674
citation: GKZ398
citation: pmcid:PMC6602470
citation: pubmed:31106358
description: Analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies.
feature list: operation 3186
feature list: operation 3206
feature list: operation 3207
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: https://orcid.org/0000-0002-2953-7982
primary contact: Stephan Pabinger

Efficient Bayesian protein inference (EPIFANY)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2269
citation: acs.jproteome.9b00566
citation: https://doi.org/10.1101/734327
citation: pmcid:PMC7583457
citation: pubmed:31975601
description: EPIFANY is a protein inference engine based on a Bayesian network.
feature list: operation 3649
feature list: operation 3767
operating system: Linux
operating system: Mac
operating system: Windows

EPIGENE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Script
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3173
application sub category: topic 3512
citation: https://doi.org/10.1101/2019.12.17.878454
description: genome wide transcription unit annotation using a multivariate probabilistic model of histone modifications. EPIGENE models the observed combination of histone modifications using a product of independent Bernoulli random variables, to identify active transcription units. Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) Network — Epigenomics. Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) Network. The network is funded by the Canadian Institutes of Health Research (CIHR) and Genome Canada and is run by epigenetics researchers from across Canada. CEEHRC is Canada's contribution to the International Human Epigenome Consortium (IHEC)
feature list: operation_0417
feature list: operation_0463
feature list: operation 3800
license: MIT

EPIP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Script
application sub category: topic_0102
application sub category: topic_0749
application sub category: topic 3168
citation: btz641
citation: pmcid:PMC7963088
citation: pubmed:31410461
description: A novel approach for condition-specific enhancer-promoter interaction prediction.
feature list: operation_0272
feature list: operation 2492
feature list: operation 3901

EPIVAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3168
application sub category: topic 3474
citation: BTZ694
citation: pubmed:31588505
description: Identifying enhancer-promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism. EPIVAN(Promoter-Enhancer Interaction predictor with pre-trained Vector and Attention based neural Networks). EPIVAN is a new deep learning method that enables predicting long-range EPIs using only genomic sequences
feature list: operation_0440
feature list: operation 3435

ERINS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 3168
citation: TCBB.2019.2954315
citation: pubmed:31751246
description: Novel Sequence Insertion Detection by Constructing an Extended Reference. Next generation sequencing technology has led to the development of methods for the detection of novel sequence insertions (nsINS). Multiple signatures from short reads are usually extracted to improve nsINS detection performance. However, characterization of nsINSs larger than the mean insert size is still challenging. This paper presents a new method, ERINS, to detect nsINS contents and genotypes of full spectrum range size. It integrates the features of structural variations and mapping states of split reads to find nsINS breakpoints, and then adopts a left-most mapping strategy to infer nsINS content by iteratively extending the standard reference at each breakpoint. Finally, it realigns all reads to the extended reference and infers nsINS genotypes through statistical testing on read counts. We test and validate the performance of ERINS on simulation and real sequencing datasets.
feature list: operation 3196
feature list: operation 3199
feature list: operation 3435

EROS-DOCK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2275
application sub category: topic 3318
citation: btz434
citation: pubmed:31125060
description: Protein-Protein Docking Using Exhaustive Branch-and-Bound Rotational Search.
feature list: operation_0482
feature list: operation 3899
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Isaure Chauvot de Beauchêne

ETI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3168
application sub category: topic 3399
citation: https://doi.org/10.1101/129387
citation: journal.pcbi.1005775
citation: pmcid:PMC5638550
citation: pmcid:PMC6735795
citation: pubmed:28968389
description: A unique tool to help understand HIV prevention among high-risk young women in Ukraine | Estimate time since infection from NGS diversity

ETM-DB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 3403
application sub category: topic 3407
application sub category: topic 3423
citation: S12906-019-2634-1
citation: pmcid:PMC6692943
citation: pubmed:31412866
description: Iintegrated Ethiopian traditional herbal medicine and phytochemicals database | ETM-DB is a free, online relational database containing Ethiopian herbal medicine, related compounds and target gene/proteins. Ethiopia is endowed with an affluence of botanical remedies that have proven useful over a long time, especially in the rural areas where modern health care is much less accessible. It is estimated that about 80% of the Ethiopian population, predominantly in the rural areas, use traditional medicine. There are about 6,500-7,500 plant species in Ethiopia, of which an estimated 12% are endemic to Ethiopia
feature list: operation 3280
feature list: operation 3803

EVE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3382
application sub category: topic 3855
citation: https://doi.org/10.1101/729434
description: A Low-Cost, Open Source, Self-Contained Bacterial EVolutionary biorEactor (EVE)
feature list: operation 3798
license: MIT

EVR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0621
application sub category: topic_0654
application sub category: topic 3810
citation: S12864-019-6096-0
citation: pmcid:PMC6794827
citation: pubmed:31615397
description: EVR is a chromosome 3D structure reconstruction tool using an Error-Vector Resultant algorithm based on DNA interaction data. With normalized or unnormalized IF matrix as input, the program generate a chromosome 3D structure output in a .pdb file. Using Cython and OpenCL, the program can run on CPUs/GPUS/APUs and thus usually faster than similar tools.
feature list: operation_0335
feature list: operation 3435
license: GPL-3.0

EVcouplings
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic_0820
application sub category: topic 2275
citation: https://doi.org/10.1101/791293
description: Proteome-scale discovery of protein interactions with residue-level resolution using sequence coevolution. Evolutionary couplings from protein and RNA sequence alignments. If you are simply interested in using EVcouplings as a library, installing the Python package is all you need to do (unless you use functions that depend on external tools). If you want to run the evcouplings application (alignment generation, model parameter inference, structure prediction, etc.) you will also need to follow the sections on installing external tools and databases. Predict protein structure, function and mutations using evolutionary sequence covariation.
feature list: operation_0272
feature list: operation_0477
feature list: operation_0478
feature list: operation 2492
license: MIT

EVlncRNA-pred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0659
application sub category: topic_0780
application sub category: topic 3512
citation: https://doi.org/10.1101/634345
description: Predicting functional long non-coding RNAs validated by low throughput experiments.
feature list: operation_0525
feature list: operation 2495
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Jihua Wang
primary contact: Yaoqi Zhou

EWAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0625
application sub category: topic 3295
application sub category: topic 3517
citation: bty163
citation: pmcid:PMC6061808
citation: pubmed:29566144
description: Epigenome-wide association study software.
feature list: operation 3196
feature list: operation 3659
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: service.html
primary contact: Fanwu Kong
primary contact: Liangde Xu
primary contact: Yongshuai Jiang

EWAS Data Hub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
application sub category: topic_0625
application sub category: topic_0654
application sub category: topic 2640
application sub category: topic 3295
application sub category: topic 3518
citation: gkz840
citation: pmcid:PMC6943079
citation: pubmed:31584095
description: A resource of DNA methylation array data and metadata.
feature list: operation 2422
feature list: operation 3186
feature list: operation 3207
software help: documentation

EWCA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0108
application sub category: topic_0128
application sub category: topic 3957
citation: S12859-019-3007-Y
citation: pmcid:PMC6744658
citation: pubmed:31521132
description: A Python script for identifying protein complexes based on an edge weight algorithm and core-attachment structure.
feature list: operation_0277
feature list: operation 2492
feature list: operation 3439

EXPANDER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 3170
application sub category: topic 3308
citation: J.JMB.2019.05.013
citation: pubmed:31100387
description: EXPANDER (EXPression ANalyzer and DisplayER) is a comprehensive software package for analysis of expression data.
feature list: operation 3223
feature list: operation 3501
feature list: operation 3680
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: manual.html

Easy-HLA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 2830
application sub category: topic 3421
citation: btz875
citation: pmcid:PMC8248894
citation: pubmed:31750874
description: A validated web application suite to reveal the full details of HLA typing. Nomenclature for Factors of the HLA System. The WHO Nomenclature Committee for Factors of the HLA System comprises the following individuals:. EasyMatch-R is a tool designed to find unrelated donors in silico. We aim to improve efficiency by saving time and resources in HLA labs. From a patient’s HLA typing in input, Easymatch-R displays probability of finding a potential unrelated bone marrow donor according to the required matching level. In addition to the number of expected donors, Easymatch-R provides complementary typings recomendations. HLA-Upgrade uses the power of haplotypes to predict full high resolution HLA-A, B, C, DRB1, DQB1 genotypes.
feature list: operation_0487
feature list: operation 3196
feature list: operation 3557

EasyMEG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3382
citation: J.CMPB.2019.105199
citation: pubmed:31743827
description: An easy-to-use toolbox for MEG analysis. an easy-to-use software for MEG analysis based on FieldTrip and Matlab GUI. You can use the editor on GitHub to maintain and preview the content for your website in Markdown files
license: GPL-3.0

EasyModel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic 2259
application sub category: topic 3315
citation: BTZ659
citation: pubmed:31504183
description: A user-friendly tool for building and analysis of simple mathematical models in systems biology
feature list: operation 2426
feature list: operation 3096
feature list: operation 3798
license: GPL-3.0

EcRBPome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0121
application sub category: topic 2275
application sub category: topic 3277
citation: S12864-019-5755-5
citation: pmcid:PMC6530084
citation: pubmed:31117939
description: Comprehensive database of Escherichia coli RNA-binding proteins (RBPs). This database documents RBPs identified by genome-wide survey of all known complete E. coli proteomes. EcRBPome also presents a cross-strain comparative account of these RBPs, as well as the constituent RNA-binding domains (RBDs).
feature list: operation 3431
feature list: operation 3501
feature list: operation 3901
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.pl
primary contact: https://orcid.org/0000-0002-6642-2367

EcoPrestMet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0202
application sub category: topic 3172
application sub category: topic 3375
citation: j.molcel.2019.04.001
citation: pmcid:PMC6591011
citation: pubmed:31047795
description: Metabolomics-Driven Exploration of the Chemical Drug Space to Predict Combination Antimicrobial Therapies.
feature list: operation 3482
feature list: operation 3629
is accessible for free: true
license: CC-BY-NC-4.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Mattia Zampieri

EdgeScaping
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3382
citation: JOURNAL.PONE.0220279
citation: pmcid:PMC6684082
citation: pubmed:31386677
description: Mapping the spatial distribution of pairwise gene expression intensities | This file details the different codes that we utlized to create the results for EdgeScaping
feature list: operation_0313
feature list: operation 3463
feature list: operation 3766
license: MIT

El-MAVEN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 3172
application sub category: topic 3520
citation: 978-1-4939-9236-2 19
citation: pubmed:31119671
description: Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics.
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation

Electric Guru
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3334
description: Program for neurofeedback that supports modularEEG. Uses fast Fourier transform to extract frequency bands from the raw signal.
is accessible for free: true
operating system: Windows

ElemCor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0154
application sub category: topic 3407
application sub category: topic 3520
citation: s12859-019-2669-9
citation: pmcid:PMC6381631
citation: pubmed:30782135
description: Software tool to correct LC-MS data in isotope labeling experiments.
feature list: operation 3629
feature list: operation 3632
feature list: operation 3638
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Di Du
primary contact: Xiaoyang Su

Emap2sec
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0736
application sub category: topic 3382
application sub category: topic 3542
citation: S41592-019-0500-1
citation: pmcid:PMC6717539
citation: pubmed:31358979
description: Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning | Emap2sec is a computational tool to identify protein secondary structures | Emap2sec is a computational tool using deep learning that can accurately identify protein secondary structures, alpha helices, beta sheets, others (coils/turns), in cryo-Electron Microscopy (EM) maps of medium to low resolution
feature list: operation_0468
feature list: operation_0470
feature list: operation 2488
license: GPL-3.0

EnClaSC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3474
citation: https://doi.org/10.1101/754085
citation: s12859-020-03679-z
citation: pmcid:PMC7496207
citation: pubmed:32938367
description: A novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes | Abstract Background In recent years, the rapid development of single-cell RNA-sequencing (scRNA-seq) techniques enables the quantitative characterization of cell types at a single-cell resolution. With the explosive growth of the number of cells profiled in individual scRNA-seq experiments, there is a demand for novel computational methods for classifying newly-generated scRNA-seq data onto annotated labels. Although several methods have recently been proposed for the cell-type classification of single-cell transcriptomic data, such limitations as inadequate accuracy, inferior robustness, and low stability greatly limit their wide applications. Results We propose a novel en semble approach, named EnClaSC, for accurate and robust cell-type cla ssification of s ingle- c ell transcriptomic data
feature list: operation 3891

EnImpute
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0099
application sub category: topic 3474
citation: BTZ435
citation: pubmed:31125056
description: R package for imputing dropout events in single cell RNA sequencing data via ensemble learning.
feature list: operation 3192
feature list: operation 3557
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: EnImpute-manual.pdf
primary contact: Xiao-Fei Zhang

EnTAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: https://doi.org/10.1111/1755-0998.13106
citation: pubmed:31628884
description: Bringing faster and smarter functional annotation to non-model eukaryotic transcriptomes.
feature list: operation_0362
feature list: operation_0524
feature list: operation 3192
feature list: operation 3258
feature list: operation 3501
software help: latest

EncyclopeDIA
type: SoftwareApplication
input: Sequence set
  type: FormalParameter
  additional type: data_0850
  encoding format: format 1929
input: Mass spectrometry spectra
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3621
input: Mass spectrometry spectra
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3246
output: Peptide identification
  type: FormalParameter
  additional type: data_0945
  encoding format: format 3245
output: Mass spectrometry spectra
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3621
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic 3520
citation: pubmed:30510204
description: EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries.
feature list: operation_0335
feature list: operation 3215
feature list: operation 3631
feature list: operation 3646
feature list: operation 3649
feature list: operation 3860
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: EncyclopeDIA manual.pdf
software version: 0.8.1
primary contact: Brian Searle

EnhancerDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
additional type: Web application
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 2885
citation: bay141
citation: pmcid:PMC6344666
citation: pubmed:30689845
description: Database to discover the regulate relationships in the context of enhancers.
feature list: operation_0441
feature list: operation 3232
feature list: operation 3792
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: Z. Guo

Ensembl Compara
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
additional type: Web service
application sub category: topic_0080
application sub category: topic_0091
application sub category: topic_0194
application sub category: topic_0797
application sub category: topic 3293
citation: gr.073585.107
citation: pmcid:PMC2652215
citation: pubmed:19029536
description: Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.
feature list: operation_0323
feature list: operation_0324
feature list: operation_0491
feature list: operation_0492
feature list: operation_0558
feature list: operation 2403
feature list: operation 3182
feature list: operation 3460
feature list: operation 3663
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: homology method.html
software help: compara.html
software version: e56
software version: e81

Enspara
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0176
application sub category: topic 3318
citation: https://doi.org/10.1063/1.5063794
citation: pmcid:PMC6910589
citation: pubmed:30709308
description: Library for working with Markov state models (MSMs) that provides several novel algorithms and specialized data structures that dramatically improve the scalability of traditional MSM methods.
feature list: operation 2476
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: enspara
primary contact: Bowman Lab

EnteroBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0196
application sub category: topic 3305
application sub category: topic 3796
citation: gkae902
citation: mgen.0.000410
citation: https://doi.org/10.1101/727230
citation: pmcid:PMC7641423
citation: pubmed:32726198
citation: pubmed:39441072
description: Global genomic population structure of Salmonella, Escherichia/Shigella, Mycobacterium tuberculosis, Streptococcus, Clostridioides, Vibrio, Helicobacter, Yersinia, Moraxella
feature list: operation_0524
feature list: operation 3216
feature list: operation 3840
software help: about.html

Entrezpy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0084
application sub category: topic_0602
application sub category: topic 3068
citation: btz385
citation: pmcid:PMC6821292
citation: pubmed:31077305
description: Python library to dynamically interact with the NCBI Entrez databases.
feature list: operation 2421
feature list: operation 2422
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: entrezpy.readthedocs.io
primary contact: Jan buchmann

Eoulsan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3316
description: A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers. With Eoulsan, users can easily set up a cloud computing cluster and automate the analysis of several samples at once using various software solutions available. Working either on standalone workstations or cloud computing clusters, Eoulsan provides an integrated and flexible solution for RNA-Seq data analysis of differential expression.
feature list: operation 3223

EphaGen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic 3168
application sub category: topic 3512
citation: GKZ775
citation: pmcid:PMC6868350
citation: pubmed:31511888
description: Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context | Estimate NGS Dataset qualitity in terms of its ability to detect mutations of predefined spectrum | EphaGen - a package to estimate NGS Dataset qualitity in terms of its ability to detect mutations of predefined spectrum
feature list: operation 2428
feature list: operation 2929
feature list: operation 3227

Epi-GTBN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic_0625
citation: S12859-019-3022-Z
citation: pmcid:PMC6712799
citation: pubmed:31455207
description: An approach of epistasis mining based on genetic Tabu algorithm and Bayesian network
feature list: operation 3196
license: GPL-2.0

EpiAlign
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3169
application sub category: topic 3170
application sub category: topic 3173
citation: GKZ287
citation: pmcid:PMC6648345
citation: pubmed:31045217
description: Alignment-based bioinformatic tool for comparing chromatin state sequences.
feature list: operation 3501
feature list: operation 3891
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: manual.pdf
primary contact: https://orcid.org/0000-0002-9288-5648
primary contact: Haowen Zhang

EpiAlignment
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0654
application sub category: topic 3169
application sub category: topic 3173
citation: GKZ426
citation: pmcid:PMC6602515
citation: pubmed:31114924
description: Alignment of genomic regions with both sequence and epigenomic information.
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: manual.html
primary contact: Sheng Zhong

EpiCompare
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3173
citation: btx371
citation: pmcid:PMC5860030
citation: pubmed:28605501
description: Tool to define and explore genomic regions with tissue or cell type-specific epigenomic features.
feature list: operation_0438
feature list: operation 3501
feature list: operation 3798
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: EpiCompare3
software help: README.md
primary contact: Yu He

EpiEstim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web application
application sub category: topic 3305
application sub category: topic 3315
application sub category: topic 3324
application sub category: topic 3375
citation: j.epidem.2019.100356
citation: pmcid:PMC7105007
citation: pubmed:31624039
description: Improved inference of time-varying reproduction numbers during infectious disease outbreaks. This web application generates an estimate of infectious disease transmissibility throughout an outbreak. The time-dependent reproduction number (R) is inferred from disease incidence time series and patient data or estimates of the serial interval.
feature list: operation 2422
feature list: operation 2426
feature list: operation 3799
software help: EpiEstim.pdf

EpiMethEx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0749
application sub category: topic 3295
application sub category: topic 3518
citation: s12859-018-2397-6
citation: pmcid:PMC7394332
citation: pubmed:30717649
description: R package for large-scale integrated analysis in methylation hotspots linked to genetic regulation.
feature list: operation 3206
feature list: operation 3207
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows

EpiMethylTag
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3179
application sub category: topic 3295
application sub category: topic 3674
citation: S13059-019-1853-6
citation: pmcid:PMC6868874
citation: pubmed:31752933
description: EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation. Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels
feature list: operation 3186
feature list: operation 3207
feature list: operation 3222

EpiProfileLite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0154
application sub category: topic 3295
application sub category: topic 3520
citation: GR.247353.118
citation: pmcid:PMC6581051
citation: pubmed:31123082
description: Analysis of histone post-translational modifications by direct infusion mass spectrometry .
feature list: operation_0417
feature list: operation 2929
feature list: operation 3645
is accessible for free: true
license: GPL-3.0
operating system: Windows
software help: README.md
software help: User Manual of EpiProfileLite.pdf
primary contact: https://orcid.org/0000-0001-9073-6641

EpiSAFARI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3295
citation: btz702
citation: pmcid:PMC7703766
citation: pubmed:31501853
description: Sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements | EpiSAFARI: Sensitive Detection of Valley Shaped Patterns in Epigenetic Signal Profiles | EpiSAFARI is a command line tool for detection, annotation, and characterization of the valley shaped patterns within the functional genomics signal profiles. It takes:
feature list: operation_0441
feature list: operation 3222
feature list: operation 3501

EpiSmokEr
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3674
citation: EPI-2019-0206
citation: pubmed:31466478
description: A robust classifier to determine smoking status from DNA methylation data | Aim: Smoking strongly influences DNA methylation, with current and never smokers exhibiting different methylation profiles. Methods: To advance the practical applicability of the smoking-associated methylation signals, we used machine learning methodology to train a classifier for smoking status prediction. Results: We show the prediction performance of our classifier on three independent whole-blood datasets demonstrating its robustness and global applicability. Furthermore, we examine the reasons for biologically meaningful misclassifications through comprehensive phenotypic evaluation. Conclusion: The major contribution of our classifier is its global applicability without a need for users to determine a threshold value for each dataset to predict the smoking status
feature list: operation_0417

Epigenomics Workflow on Galaxy and Jupyter
type: SoftwareApplication
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1931
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1931
output: Sequence coordinates
  type: FormalParameter
  additional type: data 2012
  encoding format: format 3003
output: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic 3125
application sub category: topic 3173
application sub category: topic 3512
citation: zenodo.3298029
description: Reproducible Epigenomics Analysis pipeline for the analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter. The analysis workflow was originally designed to analyze Brassica rapa data.
feature list: operation 3563
feature list: operation 3677
funder: Agencia Estatal de Investigación
license: MIT
software help: epigenomics pipeline

Episo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0099
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3674
application sub category: topic 3794
citation: btz900
citation: pmcid:PMC7141862
citation: pubmed:31794005
description: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite. Episo-quantify Epitranscriptomal RNA m5c at isoform level. Episo is a probabilistic model to quantify Epitranscriptomal RNA m5C at the transcript isoform level. Episo consists of three tools, named mapper, quant and Bisulfitefq, for mapping, quantifying, and simulating RNA-BisSeq data, respectively. Episo needs a working version of Perl and it is run from the command line. Meanwhile, Bowtie, Tophat and Cufflinks need to be installed on your computer. First you need to download a transcript annotation file from the Ensembl or NCBI websites. Episo supports the reference trancriptom sequence files in FastA format, allowed file extensions are either .fa or .fasta. The details see the document Episo_User_Guide.pdf. This pakage is for estimating m5c level by using Kallisto in Episo
feature list: operation_0308
feature list: operation 2495
feature list: operation 3186
feature list: operation 3799
license: BSD-2-Clause

Epithelial Modelling Platform
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic_0602
application sub category: topic 3398
citation: https://doi.org/10.1101/631465
description: Tool for Model Discovery and Assembly with the Physiome Model Repository.
feature list: operation_0337
feature list: operation 3096
feature list: operation 3431
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Dewan M. Sarwar

ErrorTracer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic 2269
application sub category: topic 3407
citation: btz761
citation: pmcid:PMC7703767
citation: pubmed:31598631
description: ModelExplorer is a metabolic model visualization package that can assist the user in finding blocked parts of the metabolic network as well as finding out why they are blocked.
feature list: operation_0481
feature list: operation 3660

EuRBPDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
application sub category: topic_0099
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic_0621
application sub category: topic 2640
citation: gkz823
citation: pmcid:PMC6943034
citation: pubmed:31598693
description: A comprehensive database for eukaryotic RNA binding proteins. EuRBPDB is a comprehensive and user-friendly database for eukaryotic RNA binding proteins (RBPs). It contains 315,222 RBPs (forms 6,368 ortholog groups) from 162 eukaryotic species, including human, mouse, fly, worm and yeast. EuRBPDB provides precise and comprehensive list of RBPs of each eukaryote with annotations collected from various public databases
feature list: operation_0306
feature list: operation 2421
feature list: operation 3902

EuroForMix
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2885
citation: j.fsigen.2015.11.008
citation: pubmed:26720812
description: Open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts.
feature list: operation 3196
feature list: operation 3227
feature list: operation 3629
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 2.1.0

EventEpi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0218
application sub category: topic 3301
application sub category: topic 3305
citation: https://doi.org/10.1101/19006395
citation: journal.pcbi.1008277
citation: pmcid:PMC7717563
citation: pubmed:33216746
description: EventEpi - A Natural Language Processing Framework for Event-Based Surveillance - is a tool to extract the most important entites from a epidemiological text and to analyze them.
feature list: operation 3280

Evidence Based Microbial Associations Miner (EviMass)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0218
application sub category: topic_0634
application sub category: topic 3174
application sub category: topic 3697
citation: FGENE.2019.00849
citation: pmcid:PMC6763948
citation: pubmed:31616466
description: A Literature Evidence-Based Miner for Human Microbial Associations. The importance of understanding microbe-microbe as well as microbe-disease associations is one of the key thrust areas in human microbiome research
feature list: operation_0224
feature list: operation_0306
feature list: operation_0337
software help: user manual.pdf

EvidenceAggregatedDriverRanking
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3517
citation: BTZ365
citation: pmcid:PMC6612835
citation: pubmed:31510680
description: Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation | Ranking methodology of potential Driver genes using multi-view feature sets
feature list: operation 3436
feature list: operation 3501
feature list: operation 3766
license: Apache-2.0

EvidenceModeler
type: SoftwareApplication
input: Gene report
  type: FormalParameter
  additional type: data_0916
  encoding format: format 1209
input: Evidence
  type: FormalParameter
  additional type: data 2042
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0114
application sub category: topic_0203
description: The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.
feature list: operation 2454

EvoClustRNA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0099
application sub category: topic 2814
application sub category: topic 3170
citation: S12859-019-3120-Y
citation: pmcid:PMC6806525
citation: pubmed:31640563
description: RNA 3D structure prediction guided by independent folding of homologous sequences and multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io.
feature list: operation_0278
feature list: operation_0295
feature list: operation_0303
feature list: operation_0476
feature list: operation 2441
license: GPL-3.0
software help: evoclustrna.rtfd.io

EvoEF2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic_0736
application sub category: topic 3318
citation: btz740
citation: pmcid:PMC7144094
citation: pubmed:31588495
description: Accurate and fast energy function for computational protein design. energy potential for protein design. EvoEF is a composite energy force field that contains two versions. The first version, EvoEF1, includes five energy terms with parameters optimized on two large sets of thermodynamics mutation data (ΔΔGstability and ΔΔGbind), while the second version, EvoEF2, includes nine energy terms and optimized based on recapitulation of protein sequence design. Extensive benchmark and analysis showed that the usefulness of energy functions is highly correlated with the parameter optimization processes. While EvoEF1 performs better than EvoEF2 on ΔΔG estimation, EvoEF2 significantly outperforms EvoEF2 on de novo protein sequence design. Therefore, we suggest users download the two versions according to their own needs.
feature list: operation_0303
feature list: operation_0480
feature list: operation 2492
feature list: operation 3644
license: MIT

EvoFreq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2640
application sub category: topic 3168
application sub category: topic 3293
citation: https://doi.org/10.1101/743815
citation: s12859-019-3173-y
citation: pmcid:PMC6916070
citation: pubmed:31842729
description: Visualization of the Evolutionary Frequencies of Sequence and Model Data | Evolutionary frequency visualization tool of temporal data | Users have options ot install EvoFreq depending on if they want to use 'devtools'. Below we show two popular methods for installation. You will need a fully operational install of R (≥3.5.0) and, optionally, RStudio | Visualization Package for Evolutionary Dynamics from Sequence and Model Data. biorxiv pre-print here
feature list: operation_0337
feature list: operation 1812
feature list: operation 3196
license: GPL-3.0

EvoPPI
type: SoftwareApplication
input: Gene identifier
  type: FormalParameter
  additional type: data 1025
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0128
author: https://orcid.org/0000-0001-8749-2703
author: https://orcid.org/0000-0002-6476-7206
author: Noé Vázquez
citation: 978-3-319-98702-6 18
citation: s12539-019-00317-y
citation: pubmed:30707359
contributor: https://orcid.org/0000-0001-7032-5220
contributor: https://orcid.org/0000-0002-3943-8013
description: EvoPPI allows the easy comparison of publicly available data from the main Protein-Protein Interaction (PPI) databases for the same and distinct species.
feature list: operation 2422
primary contact: https://orcid.org/0000-0002-7139-2107

EvolClust
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0623
application sub category: topic 3407
citation: j.jmb.2023.168013
citation: btz706
citation: pmcid:PMC7703780
citation: pubmed:31560365
citation: pubmed:36806474
description: EvolClust predicts groups of genes that are conserved in terms of gene order across different species distinguishing it from the background gene order conservation found between species. We define a cluster as a group of homologous proteins that are found grouped together in at least two different genomes and which are more conserved than what is expected for the pair of genomes. The order of the genes inside the cluster is not necessarily conserved. Pairwise clusters are grouped into multi-species families.
feature list: operation 2422
feature list: operation 3432
software version: 1.0

EvryRNA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0659
description: EvryRNA platform is a web server providing various algorithms and bioinformatics tools developed in the laboratory IBISC of UEVE/Genopole, and dedicated to the prediction and the analysis of non-coding RNAs (ncRNAs).

ExMS2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: ACS.ANALCHEM.9B01682
citation: pubmed:31082210
description: Integrated Solution for Hydrogen-Deuterium Exchange Mass Spectrometry Data Analysis.
feature list: operation 2929
feature list: operation 3627
feature list: operation 3631
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: ExMSTutorial 09292011.pdf

ExaML
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0194
application sub category: topic 3068
citation: btv184
citation: pmcid:PMC4514929
citation: pubmed:25819675
description: Tool for phylogenomic analyses on supercomputers.
feature list: operation_0547
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: ExaML.pdf
software version: 3.0
primary contact: Alexandros Stamatakis

ExaStoLog
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 2269
application sub category: topic 3068
application sub category: topic 3292
citation: https://doi.org/10.1101/794230
citation: s12859-020-03548-9
citation: pmcid:PMC7291460
citation: pubmed:32527218
description: Exact calculation of stationary solution and parameter sensitivity analysis of stochastic continuous time Boolean models. Abstract Motivation Solutions to stochastic Boolean models are usually estimated by Monte Carlo simulations, but as the state space of these models can be enormous, there is an inherent uncertainty about the accuracy of Monte Carlo estimates and whether simulations have reached all asymptotic solutions. Moreover, these models have timescale parameters (transition rates) that the probability values of stationary solutions depend on in complex ways that have not been analyzed yet in the literature. These two fundamental uncertainties call for an exact calculation method for this class of models.
feature list: operation 2426
feature list: operation 3435
feature list: operation 3659
license: LGPL-3.0

Exautomate
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3676
citation: https://doi.org/10.1101/649368
description: User-friendly tool for region-based rare variant association analysis (RVAA).
feature list: operation 3196
feature list: operation 3211
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: README.md

ExonSkipDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3320
application sub category: topic 3512
citation: gkz917
citation: pmcid:PMC7145592
citation: pubmed:31642488
description: Functional annotation of exon skipping event in human. Exon skipping (ES), the most common alternative splicing event, has been reported to contribute to diverse human diseases due to the loss of functional domains sites or frame shifting of open reading frame (ORF) and noticed as therapeutic targets
feature list: operation_0436
feature list: operation_0446
feature list: operation 2436

ExpansionHunter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3673
citation: btz431
citation: pmcid:PMC6853681
citation: pubmed:31134279
description: Sequence-graph-based tool to analyze variation in short tandem repeat regions.
feature list: operation 3196
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: 01 Introduction.md
primary contact: Illumina Open Source Software

ExpansionHunter Denovo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Suite
application sub category: topic_0102
application sub category: topic_0157
application sub category: topic_0196
application sub category: topic 2885
citation: https://doi.org/10.1101/863035
citation: s13059-020-02017-z
citation: pmcid:PMC7187524
citation: pubmed:32345345
description: A computational method for locating known and novel repeat expansions in short-read sequencing data. A suite of tools for detecting expansions of short tandem repeats. ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs). EHdn is intended for analysis of a collection of BAM/CRAM files containing alignments of short (100-200bp) reads.
feature list: operation_0379
feature list: operation 3196
feature list: operation 3198
license: Apache-2.0
software help: 00 Introduction.md

Expedition
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic 3320
citation: j.molcel.2017.06.003
citation: pmcid:PMC5540791
citation: pubmed:28673540
description: Suite for single-cell alternative splicing analysis. Consists of outrigger, anchor and bonvoyage.
feature list: operation 2499
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows

ExploreASL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3379
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3452
citation: j.neuroimage.2020.117031
citation: https://doi.org/10.1101/845842
citation: pubmed:32526385
description: an image processing pipeline for multi-center ASL perfusion MRI studies. ExploreASL is a pipeline and toolbox for image processing and statistics of arterial spin labeling perfusion MR images. It is designed as a multi-OS, open source, collaborative framework that facilitates cross-pollination between image processing method developers and clinical investigators. OSIPI ASL pipelines google forms. QUIZ: Presentation, QUIZ + IMAGES
feature list: operation 3435
feature list: operation 3443
feature list: operation 3799
software help: index.html

Exposome Explorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 2640
application sub category: topic 3172
application sub category: topic 3305
application sub category: topic 3360
application sub category: topic 3390
citation: gkz1009
citation: pmcid:PMC7145555
citation: pubmed:31724701
description: An update incorporating candidate dietary biomarkers and dietary associations with cancer risk. database on biomarkers of environmental exposures. First database dedicated to biomarkers of exposure to environmental risk factors for diseases. BiomarkersConcentrationsAssociations with cancer risk. The database is being actively updated.
feature list: operation 2421
software version: 2.0

EzClermont
type: SoftwareApplication
input: Sequence assembly
  type: FormalParameter
  additional type: data_0925
  encoding format: format 1929
output: Text
  type: FormalParameter
  additional type: data 3671
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: https://doi.org/10.1101/317610
description: Easy interface for determining the Clermont 2013 phylotype of an E. coli isolate
feature list: operation 3478
primary contact: https://orcid.org/0000-0002-9035-2143

FACEPAI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Workflow
application sub category: topic_0091
application sub category: topic_0632
application sub category: topic_0654
application sub category: topic 3168
citation: S12898-019-0269-1
citation: pmcid:PMC6896590
citation: pubmed:31810454
description: A script for fast and consistent environmental DNA processing and identification. Scripts for executing a filtering, clustering and identification pipeline for eDNA samples. Fast And Consistent Environmental-DNA Processing And Identification (& Conversion and Preparation of Reference Sequences). Wahlberg, E. 2019. FACEPAI: a script for fast and consistent environmental DNA processing and identification. BMC Ecology 19: 51, doi:10.1186/s12898-019-0269-1
feature list: operation 2422
feature list: operation 3431
feature list: operation 3695
license: GPL-3.0

FAConstructor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3315
application sub category: topic 3382
citation: s11548-019-02053-6
citation: pmcid:PMC6851223
citation: pubmed:31401715
description: An interactive tool for geometric modeling of nerve fiber architectures in the brain | The fiber arcitecture constructor (FAConstructor) allows a simple and effective creation of fiber models based on mathematical functions or the manual input of data points. Models are visualized during creation and can be interacted with by translating them in the 3-dimensional space
feature list: operation_0337
license: GPL-3.0

FAIR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic 3070
application sub category: topic 3518
citation: https://doi.org/10.1101/739334
description: Two real use cases of FAIR maturity indicators in the life sciences | This repository contains the results of the FAIR Metrics Group | FAIR Maturity Indicators and Tools | [Horizon 2020 Commission expert group on Turning FAIR data into reality](http://ec.europa.eu/transparency/regexpert/index.cfm?do=groupDetail.groupDetail&groupID=3464
feature list: operation 2422
feature list: operation 3431
feature list: operation 3501
license: MIT

FAIRDataPoint
type: SoftwareApplication
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 3256
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 3956
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 3256
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic_0089
application sub category: topic_0605
author: 0000-0002-1215-167X
author: Kees burger
citation: dint a 00031
contributor: 0000-0002-1215-167X
contributor: Kees burger
contributor: Mark Thompson
description: FAIRDataPoint is a REST api for creating, storing and servering FAIR metadata. The metadata contents are in this api are generated semi-automatically according to the FAIR Data Point software specification document. In the current version of api we support GET, POST and PATCH requests.
feature list: operation_0226
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: wiki
primary contact: https://orcid.org/0000-0002-1164-1351
primary contact: 0000-0002-1215-167X

FAIR Data tools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic 3071
description: The Data FAIRport includes FAIRifier and Metadata Editor (to create), FAIR Data Point (to publish), FAIR Search Engine (to find), ORKA (to annotate) FAIR data descriptions.
primary contact: Rob Hooft

FAIR Search Engine
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3077
description: FAIR search engine, designed as a prototype for finding FAIR resources.
is accessible for free: true
license: MIT

FAIRifier
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0219
application sub category: topic 3345
description: A general-purpose FAIRifier on the basis of the OpenRefine data cleaning and wrangling tool and the RDF plugin. This FAIRifier enables a post-hoc FAIRification workflow: load an existing dataset, perform data wrangling tasks, add FAIR attributes to the data, generate a linked data version of the data and, finally, push the result to an online FAIR data infrastructure to make it accessible and discoverable. Literal values in a dataset can be replaced by identifiers either manually or by embedded, customizable script expressions. The interoperability of the dataset can be improved by connecting these identifiers into a meaningful semantic graph-structure of ontological classes and properties using the integrated RDF model editor. A provenance trail automatically keeps track of each modification and additionally enables “undo” operations and repetition of operations on similar datasets. A FAIR data export function opens up a metadata editor to provide information about the dataset itself.
is accessible for free: true

FAME 3
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic_0154
application sub category: topic 3375
application sub category: topic 3407
citation: ACS.JCIM.9B00376
citation: pubmed:31361490
description: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes | In this work we present the third generation of FAst MEtabolizer (FAME 3), a collection of extra trees classifiers for the prediction of sites of metabolism (SoMs) in small molecules such as drugs, druglike compounds, natural products, agrochemicals, and cosmetics. FAME 3 was derived from the MetaQSAR database ( Pedretti et al. J. Med. Chem. 2018 , 61 , 1019 ), a recently published data resource on xenobiotic metabolism that contains more than 2100 substrates annotated with more than 6300 experimentally confirmed SoMs related to redox reactions, hydrolysis and other nonredox reactions, and conjugation reactions
feature list: operation 2939
feature list: operation 3454
feature list: operation 3891

FAMoS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic 2269
citation: JOURNAL.PCBI.1007230
citation: pmcid:PMC6697322
citation: pubmed:31419221
description: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics | Most biological systems are difficult to analyse due to a multitude of interacting components and the concomitant lack of information about the essential dynamics. Finding appropriate models that provide a systematic description of such biological systems and that help to identify their relevant factors and processes can be challenging given the sheer number of possibilities. Model selection algorithms that evaluate the performance of a multitude of different models against experimental data provide a useful tool to identify appropriate model structures
feature list: operation 2426
feature list: operation 3891
license: MIT
software help: FAMoS.pdf

FARDEEP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 3474
application sub category: topic 3518
citation: JOURNAL.PCBI.1006976
citation: pmcid:PMC6522071
citation: pubmed:31059559
description: Fast And Robust DEconvolution of Expression Profiles (FARDEEP) - machine learning tool for enumerating immune cell subsets from whole tumor tissue samples.
feature list: operation 2495
feature list: operation 3192
feature list: operation 3629
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-1049-2219
primary contact: https://orcid.org/0000-0002-9868-9824

FARFAR2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0659
application sub category: topic 3512
citation: j.str.2020.05.011
citation: https://doi.org/10.1101/764449
citation: pmcid:PMC7415647
citation: pubmed:32531203
description: Improved de novo Rosetta prediction of complex global RNA folds | ROSIE Rosetta server based on www.rosettacommons.org engine | Welcome to ROSIE Rosetta Online Server that Includes Everyone | Please cite the following article when referring to results from our ROSIE server: | Watkins, A. M.; Das, R. "An automated and customizable RNA fragment assembly protocol in Rosetta. bioRxiv 223305; doi: https://doi.org/10.1101/223305
feature list: operation_0278
feature list: operation_0476
feature list: operation_0483
software help: documentation

FASTA API (EBI)
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
output: Sequence search results
  type: FormalParameter
  additional type: data_0857
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0080
citation: pnas.85.8.2444
citation: pmcid:PMC280013
citation: pubmed:3162770
description: FASTA stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison.
feature list: operation_0346
feature list: operation 2451
operating system: Linux
operating system: Mac
operating system: Windows
software help: fasta rest
software version: 1

FASTA (EBI)
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
output: Sequence search results
  type: FormalParameter
  additional type: data_0857
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0080
author: Bill Pearson
citation: 0888-7543(91)90071-L
citation: gkac240
citation: gkae241
citation: pmcid:PMC11223882
citation: pmcid:PMC9252731
citation: pubmed:35412617
citation: pubmed:38597606
description: Sequence similarity searching against protein databases. FASTX and FASTY translate a DNA query. Optimal searches with SSEARCH (local), GGSEARCH (global) and GLSEARCH (global query, local database).
feature list: operation_0346
feature list: operation 2451
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
provider: University of Virginia
software help: terms-of-use
software help: fasta36
software help: help
software version: 1
primary contact: Job Dispatcher

FASTO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Ontology
application sub category: topic_0089
application sub category: topic 3400
application sub category: topic 3421
citation: S12911-019-0806-Z
citation: pmcid:PMC6511155
citation: pubmed:31077222
description: FHIR And SSN based Type 1 diabetes Ontology (FASTO) is an OWL 2 ontology for real time management of insulin for diabetes patients especially type 1 diabetics.
feature list: operation 3352
feature list: operation 3501
feature list: operation 3559
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-9559-4352

FASTX::Reader
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
  encoding format: format 1929
  encoding format: format 1930
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
description: a Perl module to parse FASTA/FASTQ files
feature list: operation 2422
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software version: 0.6

FATSLiM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0153
application sub category: topic_0820
application sub category: topic 3068
citation: btw563
description: Software to analyze Molecular Dynamics simulations of membranes.
feature list: operation 2476
feature list: operation 3279
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: fatslim
primary contact: Sébastien Buchoux

FB5P-seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic 2830
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/795575
citation: fimmu.2020.00216
citation: pmcid:PMC7062913
citation: pubmed:32194545
description: FACS-based 5-prime end single-cell RNAseq for integrative analysis of transcriptome and antigen receptor repertoire in B and T cells. FB5P-seq: FACS-based 5'-end single-cell RNA-seq. Copyright 2019: PMlab, Centre d'Immunologie de Marseille-Luminy This work is distributed under the terms of the GNU General Public License. It is free to use for all purposes. FB5P-seq is a computational pipeline to process single-cell RNA sequencing (scRNAseq) data produced with the FB5P-seq protocol designed by the Milpied lab at Centre d'Immunologie de Marseille-Luminy. The pipeline relies on 5 main softwares:
feature list: operation 3200
feature list: operation 3680
feature list: operation 3799
license: GPL-3.0

FBB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 3170
application sub category: topic 3794
citation: btw608
citation: pubmed:27663496
description: Fast Bayesian-bound tool to calibrate RNA-seq aligners.
feature list: operation 3198
feature list: operation 3627
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Ramón Huerta

FCM-m
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0610
application sub category: topic_0749
application sub category: topic 3382
author: https://orcid.org/0000-0002-2668-5808
citation: OE.27.034838
citation: pubmed:31878664
description: Optical classification of inland waters based on an improved Fuzzy C-Means method. Water optical clustering based on water color information is important for many ecological and environmental application studies, both regionally and globally. The fuzzy clustering method avoids the sharp boundaries in type-memberships produced by hard clustering methods, and thus presents its advantages. However, to make good use of the fuzzy clustering methods on water color spectra data sets, the determination of the fuzzifier parameter (m) of FCM (fuzzy c-means) is the key factor. Usually, the m is set to 2 by default. Unfortunately, this method assigned some membership degrees to non-belonging water type, failing to obtain the unitarity of cluster structure in some cases, especially in inland eutrophic water.
feature list: operation 3432
primary contact: Yunmei Li

FCNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3063
application sub category: topic 3474
citation: FGENE.2019.01009
citation: pmcid:PMC6818468
citation: pubmed:31695723
description: Measurement of Conditional Relatedness Between Genes Using Fully Convolutional Neural Network. Fully Convolutional Neural Network model. A demonstration of what can be accomplished visually through CSS-based design. If you want to visit this website, the google browser will be recommended !. The fully convolutional neural network (FCNN) model is a deep learning model based on traditional convolution neural network (CNN) model with a fully connected first layer and combines expression similarities and prior-knowledge similarities as the input
feature list: operation 3439
feature list: operation 3463
feature list: operation 3660
software help: example.html

Frequency Conservation Score (FCS)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic 3673
application sub category: topic 3676
citation: https://doi.org/10.1101/805051
description: A calculator of conservation and allele frequency for variant pathogenic prediction.
feature list: operation 3226
feature list: operation 3227
feature list: operation 3461

FConverter
type: SoftwareApplication
input: Annotation track
  type: FormalParameter
  additional type: data 3002
  encoding format: format 3016
output: Data
  type: FormalParameter
  additional type: data_0006
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3796
description: File format converter for FImpute
feature list: operation_0335
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.1

FEDRO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0203
application sub category: topic_0780
application sub category: topic 3512
citation: s12859-019-2696-6
citation: pmcid:PMC6471690
citation: pubmed:30999847
description: Software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing.
feature list: operation_0436
feature list: operation 3096
feature list: operation 3557
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Simona E. Rombo

FEV1
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3305
application sub category: topic 3399
application sub category: topic 3577
citation: J.CHEST.2019.09.003
citation: pubmed:31542453
description: An Individualized Prediction Model for Long-term Lung Function Trajectory and Risk of COPD in the General Population
software help: disclaimer.html

FEniCS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3315
application sub category: topic 3316
citation: J.JMR.2019.106611
citation: ans.2015.100.20553
citation: pubmed:31574354
description: The FEniCS Project is a collaborative project for the development of innovative concepts and tools for automated scientific computing, with a particular focus on the solution of differential equations by finite element methods.
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation

FFLtool
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic_0749
citation: BTZ929
citation: pubmed:31830251
description: A Web Server for Transcription Factor and miRNA Feed Forward Loop Analysis in Human. FFLtool is a webserver for analyzing Feed Forward Loop (FFL) regulatory motifs among transcription factors (TFs), microRNAs (miRNAs) and genes. FFLs potentially regulate thousands of target genes in facilitating spatiotemporal avoidance or noise buffering and play important roles in biological processes and diseases (see Refs. PMIDs: 20157565 and 24307685 ). It integrated TF-target data from hTFtarget and miR-target data from several predicted and validated databases. Except for identifying FFLs, FFLtools can also be used to search miR-target and TF-target information
feature list: operation_0463
feature list: operation 1781
feature list: operation 3792

FFPEcap-seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Workflow
application sub category: topic_0659
application sub category: topic_0769
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3676
citation: GR.249656.119
citation: pmcid:PMC6836741
citation: pubmed:31649055
description: Analysis pipeline for FFPEcap-seq. A method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.
feature list: operation 2495
feature list: operation 3192
feature list: operation 3211
feature list: operation 3799
license: GPL-2.0

Fungal Feature Tracker (FFT)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0610
application sub category: topic_0621
application sub category: topic_0625
application sub category: topic 3314
application sub category: topic 3382
citation: JOURNAL.PCBI.1007428
citation: pmcid:PMC6822706
citation: pubmed:31671091
description: A tool for quantitatively characterizing the morphology and growth of filamentous fungi. The FFT represents a user-friendly tool that automatically characterizes several fungal phenotypes using images that can be obtained using basic imaging devices. The FFT can be used to study different fungal species, conditions and image scales and resolutions. Relying on simple built-in image analysis functions, the FFT is able to quantitatively characterize conidiation, conidia morphology and different aspects of the mycelium, including the growth area, number of hyphal tips and total length of the hyphae. In addition, we developed a function within the FFT that can detect and count traps developed by nematode-trapping fungi.
feature list: operation 3443
feature list: operation 3799

FGTpartitioner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0194
application sub category: topic 2885
application sub category: topic 3293
citation: https://doi.org/10.1101/644088
description: Method for parsimonious delimitation of ancestry breakpoints in large genome-wide SNP datasets.
feature list: operation_0487
feature list: operation 3196
feature list: operation 3454
is accessible for free: true
license: WTFPL
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Tyler K. Chafin

FHIR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0089
application sub category: topic 3063
application sub category: topic 3324
application sub category: topic 3400
application sub category: topic 3489
citation: S41666-018-0043-8
citation: https://doi.org/10.2196/15199
citation: pmcid:PMC6784845
citation: pmcid:PMC6913576
citation: pubmed:31598581
citation: pubmed:31621639
description: FHIR is a standard for health care data exchange. It is a platform specification that defines a set of capabilities use across the healthcare process, in all jurisdictions, and in lots of different contexts.
feature list: operation_0337
feature list: operation 2421
feature list: operation 2422
feature list: operation 3192
feature list: operation 3891
software help: documentation.html
software help: modules.html
software version: 4.0.1

FINET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0780
application sub category: topic 3301
citation: https://doi.org/10.1101/733683
citation: s13104-020-05371-0
citation: pmcid:PMC7653809
citation: pubmed:33172489
description: FINET is a software to infer any network. Implemented by Julia with algorithms of stability selection and elastic-net, plus parameter optimization, finet can infer a network fast and accurately from a big data. Additionally, finet is user-friendly, only one single command line to complete all computational processes. Developed under Linux, but finet should work in any OS system. Installing and using finet becomes simple by using following instructions
feature list: operation_0277
feature list: operation 1781
feature list: operation 3439

FIREVAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3673
application sub category: topic 3676
citation: S13073-019-0695-X
citation: pmcid:PMC6916105
citation: pubmed:31847917
description: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures. FInding REliable Variants without ArTifacts. FIREVAT (FInding REliable Variants without ArTifacts) is an R package that performs variant refinement on cancer sequencing data. FIREVAT uses mutational signatures to identify sequencing artifacts and low-quality variants
feature list: operation 3227
feature list: operation 3629
feature list: operation 3675
feature list: operation 3695
license: MIT

FISIK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3382
application sub category: topic 3855
citation: J.BPJ.2019.07.050
citation: pubmed:31443908
description: Framework for the Inference of In Situ Interaction Kinetics from Single-Molecule Imaging Data | Recent experimental and computational developments have been pushing the limits of live-cell single-molecule imaging, enabling the monitoring of intermolecular interactions in their native environment with high spatiotemporal resolution. However, interactions are captured only for the labeled subset of molecules, which tends to be a small fraction. As a result, it has remained a challenge to calculate molecular interaction kinetics, in particular association rates, from live-cell single-molecule tracking data. To overcome this challenge, we developed a mathematical modeling-based Framework for the Inference of in Situ Interaction Kinetics (FISIK) from single-molecule imaging data with substoichiometric labeling
feature list: operation 2426
license: GPL-3.0

FIT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3308
application sub category: topic 3518
application sub category: topic 3855
citation: btx049
description: Statistical modeling tool for transcriptome dynamics under fluctuating field conditions.
feature list: operation 1812
feature list: operation 3659
feature list: operation 3799
is accessible for free: true
license: MPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: FIT.pdf
software help: FIT.html
software version: 0.0.6
primary contact: Koji Iwayama

FLAGdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0622
application sub category: topic_0780
description: Integrative database around plant genomes.

FLAM-seq analysis pipeline
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0749
application sub category: topic 3308
application sub category: topic 3512
citation: S41592-019-0503-Y
citation: pubmed:31384046
description: A full-length mRNA sequencing reveals principles of poly(A) tail length control | Although messenger RNAs are key molecules for understanding life, until now, no method has existed to determine the full-length sequence of endogenous mRNAs including their poly(A) tails. Moreover, although non-A nucleotides can be incorporated in poly(A) tails, there also exists no method to accurately sequence them. Here, we present full-length poly(A) and mRNA sequencing (FLAM-seq), a rapid and simple method for high-quality sequencing of entire mRNAs. We report a complementary DNA library preparation method coupled to single-molecule sequencing to perform FLAM-seq. Using human cell lines, brain organoids and Caenorhabditis elegans we show that FLAM-seq delivers high-quality full-length mRNA sequences for thousands of different genes per sample
feature list: operation_0308
feature list: operation_0428
feature list: operation 3192

FLEA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0781
application sub category: topic 3168
application sub category: topic 3293
citation: journal.pcbi.1006498
citation: pmcid:PMC6314628
citation: pubmed:30543621
description: Full-Length Envelope Analyzer (FLEA) - tool for longitudinal analysis of viral amplicons.
feature list: operation 3192
feature list: operation 3218
feature list: operation 3745
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

FLEXOR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0749
application sub category: topic 3372
citation: J.CMPB.2019.105048
citation: pubmed:31473443
description: A support tool for efficient and seamless experiment data processing to evaluate musculo-articular stiffness | FLEXOR is a multiplatform software tool to simplify traditional complex and manual procedures for MAS analysis
license: GPL-3.0

FMAPB2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0108
application sub category: topic_0736
application sub category: topic 3318
citation: acs.jpcb.9b06808
citation: pmcid:PMC7032052
citation: pubmed:31490691
description: Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform | Web Server for Calculating Protein Second Virial Coefficients | PI2PE: Protein Interface/Interior Prediction Engine | FMAPB2 implements FMAP, a method based on fast Fourier transform (FFT), to calculate second virial coefficients ( B 2 ) for proteins represented at the all-atom level in implicit solvent. FMAP stands for F FT-based M odeling of A tomistic P rotein-protein interactions. In FMAPB2, we express terms of the protein-protein inteaction energy as correlation functions, and evaluate them by FFT. These terms include steric repulsion, nonpolar attraction (in the form of a Lennard-Jones potential), and electrostatic interactions (in the form of a Debye-H&#252ckel potential)
feature list: operation_0409
feature list: operation 2929
feature list: operation 3454

FOCAL3D
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3382
citation: https://doi.org/10.1101/777722
citation: journal.pcbi.1008479
citation: pmcid:PMC7748281
citation: pubmed:33290385
description: A 3-dimensional clustering package for single-molecule localization microscopy | Single-molecule localization microscopy (SMLM) yields an image resolution 1-2 orders of magnitude below that of conventional light microscopy, resolving fine details on intracellular structure and macromolecular organization. The massive pointillistic data sets generated by SMLM require the development of new and highly efficient quantification tools. Density based clustering algorithms, such as DBSCAN, can provide spatial statistics on protein nucleic acid aggregation or dispersion while explicitly identifying macromolecular clusters. The performance of DBSCAN, however, is typically dependent upon an arbitrary, or at least highly subjective, parametric tuning of the algorithm. Moreover, DBSCAN can be computationally expensive, which makes it arduous to evaluate on large image stacks
license: GPL-3.0

Fast Optimized Community Significance (FOCS)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2269
application sub category: topic 3361
application sub category: topic 3474
author: https://orcid.org/0000-0002-1419-3056
citation: S41598-019-54708-8
citation: pmcid:PMC6895225
citation: pubmed:31804528
description: Computing the statistical significance of optimized communities in networks.
feature list: operation_0337
feature list: operation 3435
feature list: operation 3562
license: Apache-2.0
primary contact: https://orcid.org/0000-0002-1419-3056

FORECasT
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 2330
output: Report
  type: FormalParameter
  additional type: data 2048
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0080
application sub category: topic 2269
application sub category: topic 3321
application sub category: topic 3474
citation: nbt.4317
citation: pmcid:PMC6949135
citation: pubmed:30480667
description: Computational predictor of the mutations generated by repair of CRISPR-Cas9-induced double-strand breaks.
feature list: operation 2238
feature list: operation 2423
is accessible for free: true
license: CC-BY-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

FORESEE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0108
application sub category: topic_0202
application sub category: topic_0769
citation: btz145
contributor: Ali Esfahani
description: Tool for the systematic comparison of translational drug response modeling pipelines.
feature list: operation 1812
feature list: operation 3216
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ReferenceManual.pdf
software help: home
primary contact: L. Turnhoff

FORGe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic 3676
citation: s13059-018-1595-x
citation: pmcid:PMC6296055
citation: pubmed:30558649
description: Tool for ranking variants and building an optimal graph genome.
feature list: operation 3211
feature list: operation 3226
feature list: operation 3227
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md

FOntCell
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0089
application sub category: topic 2229
application sub category: topic 3067
application sub category: topic 3170
citation: https://doi.org/10.1101/850131
description: A Python package automatic computed fusion of ontologies.
license: GPL-3.0

FP-LIMS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0605
application sub category: topic_0607
application sub category: topic 3077
application sub category: topic 3572
description: FP-LIMS is a LIMS solution specialized on mass spectroscopy measurement equipment. Primary compatible device manufacturers include: Spectro / Ametek,Agilent Technologies,Analytik Jena AG,Bruker,Hitachi / Oxford Instruments,Horiba Jobin Yvon GmbH,Malvern Panalytical,Microtrac GmbH,OBLF,PerkinElmer,Thermo Fisher,Zwick. FP-LIMS was first released in 1993. Its first version was based on spectroscopy-giant Spectro's(Ametek) in-house Laboratory data management solution. Its primarily used in metallurgy & foundry QM-laboratories where it is used for audit-trailing, certification, managing the passing of data from devices to an immutable data-store as well as upwards to systems such as the SAP QM module. FP-LIMS was formerly distributed as [DIA]/DIA2000/DIAPLUS.
is accessible for free: false
license: Proprietary
operating system: Windows
provider: Philip Moerke
software help: support-faq

FP2VEC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0218
application sub category: topic_0602
application sub category: topic 3474
citation: BTZ307
citation: pubmed:31070725
description: Molecular featurizer for learning molecular properties.
feature list: operation 3216
feature list: operation 3659
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

FPbase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic_0078
application sub category: topic 3382
application sub category: topic 3520
citation: s41592-019-0352-8
citation: pubmed:30886412
description: Community-editable fluorescent protein database, cataloging an expanded range of proteins and parameters, including a new spectra viewer.
feature list: operation_0337
feature list: operation 2421
feature list: operation 3092
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.fpbase.org
software help: about
software version: 1.2.0
primary contact: Talley Lambert

FQStat
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic 3169
application sub category: topic 3170
application sub category: topic 3174
citation: S12859-019-3015-Y
citation: pmcid:PMC6694608
citation: pubmed:31416440
description: A parallel architecture for very high-speed assessment of sequencing quality metrics | BACKGROUND:High throughput DNA RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies. Quickly assessing the quality of giga-to-tera base levels of sequencing data has become a routine but important task. Identification and elimination of low-quality sequence data is crucial for reliability of downstream analysis results. There is a need for a high-speed tool that uses optimized parallel programming for batch processing and simply gauges the quality of sequencing data from multiple datasets independent of any other processing steps. RESULTS:FQStat is a stand-alone, platform-independent software tool that assesses the quality of FASTQ files using parallel programming
feature list: operation 3180
feature list: operation 3218
feature list: operation 3359
software help: FQStat documentation.pdf

FRASER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3325
application sub category: topic 3512
author: 0000-0002-1091-205X
citation: https://doi.org/10.1101/2019.12.18.866830
description: Detection of aberrant splicing events in RNA-seq data with FRASER. FRASER is a tool to detect aberrant splicing events in RNA-seq data. The method is currently avaiable as preprint here. Accompanying analysis code for the FRASER manuscript. The FRASER framework and workflow aims to assist the diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects. For a short tutorial on how to use FRASER on a dataset please use our Colab tutorial at: http://tinyurl.com/RNA-ASHG-colab. This is based on a workshop we presented at ASHG 2019. FRASER: Find RAre Splicing Events in RNA-seq. This folder contains the FRASER paper and supplementary data. This project depends on the python package wBuild and the R package FRASER. Further, we use the Leafcutter adaptation used in the Kremer et al paper, which can be found here
feature list: operation_0337
feature list: operation_0433
feature list: operation 2499
feature list: operation 3196
license: MIT

FRESA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic 2269
application sub category: topic 3474
author: 0000-0002-7556-245X
citation: https://doi.org/10.1101/733675
description: Benchmarking machine learning models for the analysis of genetic data using FRESA.CAD Binary Classification Benchmarking | Feature Selection Algorithms for Computer Aided Diagnosis | Contains a set of utilities for building and testing statistical models (linear, logistic,ordinal or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization License: GPL-2, GPL-2.1 and/or GPL-3.
feature list: operation 3196
license: LGPL-2.0
software help: FRESA.CAD.pdf

FSSP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3301
application sub category: topic 3315
application sub category: topic 3855
citation: 978-1-4939-9000-9 20
citation: pubmed:30580414
description: Food Spoilage and Safety Predictor (FSSP)
feature list: operation 2426
feature list: operation 3461
is accessible for free: true
operating system: Mac
operating system: Windows
software help: Index.htm

FTAlign
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0081
citation: BTZ609
citation: pubmed:31384919
description: Topology-independent and global protein structure alignment through an FFT-based algorithm | Fast topology-independent and global structure alignment through an FFT-based algorithm
feature list: operation_0503
feature list: operation_0509
feature list: operation_0510

FUMOSO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0202
application sub category: topic 2229
application sub category: topic 2640
application sub category: topic 3172
application sub category: topic 3407
citation: btz868
citation: pmcid:PMC7141866
citation: pubmed:31750879
description: Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells. MOTIVATION:The elucidation of dysfunctional cellular processes that can induce the onset of a disease is a challenging issue from both experimental and computational perspectives. Here we introduce a novel computational method based on the coupling between fuzzy logic modeling and a global optimization algorithm, whose aims are to (1) predict the emergent dynamical behaviors of highly heterogeneous systems in unperturbed and perturbed conditions, regardless the availability of quantitative parameters, (2) determine a minimal set of system components whose perturbation can lead to a desired system response, therefore facilitating the design of a more appropriate experimental strategy. RESULTS:We applied this method to investigate what drives K-ras induced cancer cells, displaying the typical Warburg effect, to death or survival upon progressive glucose depletion
feature list: operation 2426
feature list: operation 3799
license: GPL-2.0

FXD-CSD-GUI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2828
citation: S1600576719012159
citation: pmcid:PMC6878879
citation: pubmed:31798363
description: A graphical user interface for the X-ray-diffraction-based determination of crystallite size distributions. Bragg intensities can be used to analyse crystal size distributions in a method called FXD-CSD, which is based on the fast measurement of many Bragg spots using two-dimensional detectors. This work presents the Python-based software and its graphical user interface FXD-CSD-GUI. The GUI enables user-friendly data handling and processing and provides both graphical and numerical crystal size distribution results.
feature list: operation 2409
feature list: operation 3435
feature list: operation 3453

FaceGen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3382
application sub category: topic 3399
application sub category: topic 3500
citation: https://doi.org/10.1167/19.11.7
citation: pubmed:31532469
description: Create realistic 3D faces from photos or at random, edit with many controls, export for animation, rendering or 3D printing using a demographically diverse and customizable face space model
feature list: operation_0337
feature list: operation 3096
feature list: operation 3891
is accessible for free: false

FaceSync
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3474
application sub category: topic 3794
citation: F1000RESEARCH.18187.1
description: Open source framework for recording facial expressions with head-mounted cameras | The FaceSync toolbox provides 3D blueprints for building the head-mounted camera setup described in our paper. The toolbox also provides functions to automatically synchronize videos based on audio, manually align audio, plot facial landmark movements, and inspect synchronized videos to graph data
feature list: operation 3192
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Jin Hyun Cheong

Faerun
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0218
application sub category: topic 3047
citation: CHEMRXIV.7650071.V2
description: PubChem and ChEMBL Beyond Lipinski.
feature list: operation_0337
primary contact: https://orcid.org/0000-0003-2724-2942

FastFeatGen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic_0780
application sub category: topic 3474
author: https://orcid.org/0000-0002-8784-5406
citation: https://doi.org/10.1101/846311
description: Faster parallel feature extraction from genome sequences and efficient prediction of DNA N6-methyladenine sites. Faster parallel feature extraction from genome sequence. This is a tool for faster feature extraction from genome sequences and making efficient prediction. To build efficient prediction model, user can go through the following instructions step by step. If user only wants to predict query sequences from our built model, then just go to step Make prediction for query sequences. Currently, FastFeatGen supports text file as shown in dataset.txt file in datasets directory; however, fasta file can also be used with a simple preprocessing
feature list: operation_0224
feature list: operation_0253
primary contact: https://orcid.org/0000-0002-8784-5406

FastProNGS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 3168
citation: s12859-019-2936-9
citation: pmcid:PMC6580563
citation: pubmed:31208325
description: Fast preprocessing of next-generation sequencing reads.
feature list: operation 3192
feature list: operation 3219
feature list: operation 3237
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: README.md
primary contact: G. Zhang

FastqProcessing
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
description: Tools to deal with fastq sequences and paired-end reads.

FastqPuri
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: s12859-019-2799-0
citation: pmcid:PMC6500068
citation: pubmed:31053060
contributor: Claudio Lottaz
contributor: Julia Engelmann
contributor: Paula Pérez Rubio
description: High-performance preprocessing tool for RNA-seq data.
feature list: operation 3180
feature list: operation 3219
feature list: operation 3800
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Julia Engelmann

FawMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: An integrated Omics data warehouse for FAW, Spodoptera frugiperda
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 1.0

Fcirc
type: SoftwareApplication
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 2350
output: Expression data
  type: FormalParameter
  additional type: data 2603
  encoding format: format 3780
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0099
description: A Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs
feature list: operation_0292
feature list: operation_0361
is accessible for free: true
license: MIT
operating system: Linux
software help: readme.md
software version: 1.0.1

FeGenie
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0160
application sub category: topic_0196
application sub category: topic 3174
citation: https://doi.org/10.1101/777656
citation: fmicb.2020.00037
citation: pmcid:PMC7005843
citation: pubmed:32082281
description: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies | HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes | Please see the Wiki page for introduction and tutorial on how to use this tool | git clone https://github.com/Arkadiy-Garber/FeGenie.git | Easy Installation (if you have Conda installed) | HMM-lib directory can be found within FeGenie's main repository -t 8 means that 8 threads will be used for HMMER and BLAST. If you have less than 16 available on your system, set this number lower (default = 1)
feature list: operation_0310
feature list: operation 3798

FeatureSelect
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3474
citation: s12859-019-2754-0
citation: pmcid:PMC6446290
citation: pubmed:30943889
description: Software for feature selection based on machine learning approaches.
feature list: operation 3435
feature list: operation 3659
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: LBBSoft

FeptideDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 3292
citation: J.HELIYON.2019.E02076
citation: pmcid:PMC6656964
citation: pubmed:31372542
description: A web application for new bioactive peptides from food protein
feature list: operation_0366
feature list: operation_0482
feature list: operation 3646

Ferret
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3676
citation: btw147
citation: pmcid:PMC4937191
citation: pubmed:27153588
description: Tool to extract data from the 1000 Genomes Project.
feature list: operation_0487
feature list: operation_0488
feature list: operation 3196
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Ferret

Fertility-GRU
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0749
application sub category: topic 3474
citation: ACS.JPROTEOME.9B00411
citation: pubmed:31362508
description: Identifying Fertility-Related Proteins by Incorporating Deep-Gated Recurrent Units and Original Position-Specific Scoring Matrix Profiles | Identifying fertility-related proteins by incorporating GRU and PSSM profiles
feature list: operation 3639

Fetal XCMR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0593
application sub category: topic 3067
application sub category: topic 3444
citation: S12968-019-0539-2
citation: pmcid:PMC6532268
citation: pubmed:31118056
description: Numerical phantom for fetal cardiovascular magnetic resonance imaging.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.txt
primary contact: Chris Roy
primary contact: Christopher K. Macgowan

Fido-SNP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 2885
citation: GKZ420
citation: pmcid:PMC6602425
citation: pubmed:31114899
description: Webserver for scoring the impact of single nucleotide variants in the dog genome.
feature list: operation_0331
feature list: operation_0484
feature list: operation 3227
is accessible for free: true
license: CC-BY-NC-SA-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: https://orcid.org/0000-0002-2323-0963
primary contact: Piero Fariselli

FieldView
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic_0610
application sub category: topic_0632
application sub category: topic 3855
citation: TVCG.2019.2934282
citation: pubmed:31425088
description: Designing for Mobile and Immersive Visual Analytics in the Field | Abstract: Data collection and analysis in the field is critical for operations in domains such as environmental science and public safety
feature list: operation_0337
feature list: operation 3216
feature list: operation 3501

Fiji
type: SoftwareApplication
input: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3467
  encoding format: format 3548
  encoding format: format 3579
  encoding format: format 3591
  encoding format: format 3592
  encoding format: format 3603
  encoding format: format 3990
output: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3467
  encoding format: format 3548
  encoding format: format 3579
  encoding format: format 3591
  encoding format: format 3592
  encoding format: format 3603
  encoding format: format 3990
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
application sub category: topic 3382
citation: j.mex.2019.10.018
citation: nmeth.2019
citation: pmcid:PMC3855844
citation: pmcid:PMC6861648
citation: pubmed:22743772
citation: pubmed:31763187
description: A quantitative method to analyse F-actin distribution in cells. ImageJ, with "Batteries Included". Fiji: A batteries-included distribution of ImageJ. Fiji bundles together many popular and useful ImageJ plugins for image analysis into one installation, and automatically manages their dependencies and updating.
feature list: operation 3434
feature list: operation 3435
feature list: operation 3443
feature list: operation 3799
is accessible for free: true

FilterDCA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0196
application sub category: topic 3474
application sub category: topic 3542
citation: https://doi.org/10.1101/2019.12.24.887877
citation: journal.pcbi.1007621
citation: pmcid:PMC7577475
citation: pubmed:33035205
description: interpretable supervised contact prediction using inter-domain coevolution.
feature list: operation_0272
feature list: operation_0476
feature list: operation 2950
feature list: operation 3350

FindSV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Workflow
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 2885
application sub category: topic 3175
application sub category: topic 3673
citation: S13073-019-0675-1
citation: pmcid:PMC6836550
citation: pubmed:31694722
description: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. FindSV is a structural variation pipeline written in nextflow and python. FindSV performs variant calling using TIDDIT and CNVnator. similar variants are merged, and the variants are annotated using VEP, frequency database, genmod, and custom annotation using the annotator script. FindSV outputs one unfilered vcf file per caller, a merged and unfiltered vcf file (_Combined.vcf), as well as an annotated and filtered vcf file "_FindSV.vcf". In addition, FindSV outputs a ploidy tab file, that describes the ploidy for each chromosome.
feature list: operation_0452
feature list: operation 3196
feature list: operation 3227
feature list: operation 3695

FinisherSC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3673
citation: btv280
citation: pubmed:26040454
description: Repeat-aware tool for upgrading de novo assembly using long reads.
feature list: operation_0524
feature list: operation 3216
feature list: operation 3644
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Ka-Kit Lam

FishResp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3300
application sub category: topic 3407
citation: coz003
citation: pmcid:PMC6364290
citation: pubmed:30746152
description: R package and GUI application for analysis of aquatic respirometry data.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.3
primary contact: Sergey Morozov

Fiview
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3334
description: Digital Filter Design, Viewing and Comparison tool.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Jim Peters

FixVAF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3673
application sub category: topic 3794
citation: https://doi.org/10.1101/836171
description: Correcting reference bias from the Illumina Isaac aligner enables analysis of cancer genomes. Code to remove bias from Isaac aligned data by clipping all reads for variant positions by 5 bases and producing a modified vcf file. Support code for NGS copy number algorithms. Takes a file of locations and a [cr:b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings). Altered so that it clips all reads by n bases to reduce reference bias. python FixVaf.py [vcf file] [bam file] [fasta file]. The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg. Requires python 3 with psam installed. The project previously contained 2 equivalent implementations of allele counting code in perl and C for BAM CRAM processing
feature list: operation 3196
feature list: operation 3198
feature list: operation 3227
feature list: operation 3695
feature list: operation 3802

Flagser
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic 2229
application sub category: topic 3304
application sub category: topic 3474
citation: PREPRINTS201911.0366.V1
citation: https://doi.org/10.3390/a13010019
description: Computing Persistent Homology of Directed Flag Complexes. Computing homology of directed flag complexes (based on https://github.com/Ripser/ripser). Three modified versions of flagser from luetge/flagser. flagser computes the homology of directed flag complexes. For a more detailed description consult the documentation under docs/documentation_flagser.pdf. Copyright © 2017–2018 Daniel Lütgehetmann. For more detailed instructions, see docs/documentation_flagser.pdf. The program flagser-memory is a variant of flagser storing the full directed flag complex in memory, speeding up parts of the computation but requiring more memory
feature list: operation_0551
feature list: operation 2422
license: MIT

FlashWeave
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3174
application sub category: topic 3697
citation: J.CELS.2019.08.002
citation: pubmed:31542415
description: Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data | Inference of microbial interaction networks from large-scale heterogeneous abundance data | FlashWeave predicts ecological interactions between microbes from large-scale compositional abundance data (i.e. OTU tables constructed from sequencing data) through statistical co-occurrence or co-abundance. It reports direct associations, with adjustment for bystander effects and other confounders, and can furthermore integrate environmental or technical factors into the analysis of microbial systems
feature list: operation_0310
feature list: operation_0362
feature list: operation 2495
license: GPL-3.0

FlavoDb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic 3068
application sub category: topic 3172
application sub category: topic 3336
application sub category: topic 3390
citation: S13205-019-1962-7
citation: pmcid:PMC6823394
citation: pubmed:31696036
description: A web-based chemical repository of flavonoid compounds. Flavonoids are richly diverse polyphenolic plant secondary metabolites that are known to be crucial component of human diet. These compounds are attributed with variety of nutritional as well as therapeutic value. Flavonoids are often known for their effective antioxidant nature; however, their various other bioactivities are well established. These bioactivities mainly includes antibacterial, anti-cancer, cardio protective, promotion of immune system, anti-inflammatory and skin protection from ultra violet radiation; these properties are effectively reviewed by Tungmunnithum et al 2018.
feature list: operation_0305
feature list: operation 3216
feature list: operation 3799
feature list: operation 3891

Flint
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0102
application sub category: topic 3174
application sub category: topic 3697
citation: BTZ356
citation: pmcid:PMC6612844
citation: pubmed:31510682
description: Large scale microbiome profiling in the cloud | Main repository of the Flint project for Spark and Amazon EMR | This is the main repository of the Flint project for Amazon Web Services. Flint is a metagenomics profiling pipeline that is built on top of the Apache Spark framework, and is designed for fast real-time profiling of metagenomic samples against a large collection of reference genomes. Flint takes advantage of Spark's built-in parallelism and streaming engine architecture to quickly map reads against a large reference collection of bacterial genomes
feature list: operation_0310
feature list: operation 3198
feature list: operation 3211
license: MIT
software help: documentation.html
software help: faq.html
software help: getting started.html

FlowSculpt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0611
application sub category: topic 3398
application sub category: topic 3452
citation: C9LC00658C
citation: pubmed:31482902
description: Flowsculpt is an open-source utility for solving the inverse problem in pillar programming. That is, given a fluid flow shape, what is the pillar sequence and inlet design that will produce such a shape? Our utility uses a customizable genetic algorithm to determine optimal pillar sequence and inlet flow design for a given fluid flow shape.
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

FluNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0634
application sub category: topic_0781
application sub category: topic 3305
citation: https://doi.org/10.1080/02763869.2019.1657734
citation: pubmed:31687905
description: Tools for Influenza Activity and Surveillance. U.S. Influenza Surveillance System. Overview of Influenza Surveillance in the United States - CDC. Centers for Disease Control and Prevention. CDC twenty four seven. Saving Lives, Protecting People. FluNet is a global web-based tool for influenza virological surveillance first launched in 1997. The virological data entered into FluNet, e.g. number of influenza viruses detected by subtype, are critical for tracking the movement of viruses globally and interpreting the epidemiological data. The data at country level are publically available and updated weekly. The results are presented in various formats including tables, maps and graphs.
feature list: operation_0337
feature list: operation 2429
software help: overview.htm

FluReassort
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0602
application sub category: topic 3068
application sub category: topic 3293
application sub category: topic 3324
citation: BBZ128
citation: pubmed:31774482
description: A database for the study of genomic reassortments among influenza viruses.
feature list: operation_0323
feature list: operation_0552
feature list: operation 3431

FluView
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0634
application sub category: topic 3305
citation: https://doi.org/10.1080/02763869.2019.1657734
citation: pubmed:31687905
description: Tools for Influenza Activity and Surveillance. The Influenza Division at CDC collects, compiles and analyzes information on influenza activity year-round in the United States. FluView , a weekly influenza surveillance report, and FluView Interactive , an online application which allows for more in-depth exploration of influenza surveillance data, are updated each week. The data presented each week are preliminary and may change as more data is received
feature list: operation_0337
feature list: operation 2429

FluoroCellTrack
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 2229
application sub category: topic 3372
application sub category: topic 3382
citation: JOURNAL.PONE.0215337
citation: pmcid:PMC6493727
citation: pubmed:31042738
description: Algorithm for automated analysis of high-throughput droplet microfluidic data.
feature list: operation 3443
feature list: operation 3799
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0003-0484-5871

Fly-QMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 3382
application sub category: topic 3518
citation: https://doi.org/10.1101/775783
citation: journal.pcbi.1007406
citation: pmcid:PMC7100978
citation: pubmed:32126077
description: Automated analysis of mosaic imaginal discs in Drosophila | Fly-QMA: Quantitative Mosaic Analysis in Drosophila | Fly-QMA is part of the NU FlyEye platform for studying gene expression in the developing Drosophila eye. The package enables Quantitative Mosaic Analysis (QMA) - that is, it helps users compare expression levels between distinct clonal subpopulations within the eye epithelium
feature list: operation 2495
feature list: operation 3799
license: MIT
software help: documentation.html
software help: installation.html
software help: start.html

FlyCircuit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0602
application sub category: topic_0621
application sub category: topic 3304
application sub category: topic 3382
application sub category: topic 3474
citation: s12021-019-09443-w
citation: j.cub.2010.11.056
citation: pubmed:21129968
citation: pubmed:31797265
description: FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain.
feature list: operation 2421
feature list: operation 2940
feature list: operation 3450

Flye
type: SoftwareApplication
input: Sequence set (nucleic acid)
  type: FormalParameter
  additional type: data 1234
  encoding format: format 1930
output: Sequence set (nucleic acid)
  type: FormalParameter
  additional type: data 1234
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0196
application sub category: topic_0622
application sub category: topic 3174
application sub category: topic 3673
author: Jeffrey Yuan
author: Mikhail Kolmogorov
author: Yu Lin
citation: s41587-019-0072-8
citation: s41592-020-00971-x
citation: mgen.0.000294
citation: pmcid:PMC10699202
citation: pmcid:PMC6807382
citation: pubmed:30936562
citation: pubmed:31483244
citation: pubmed:33020656
description: Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.
feature list: operation_0523
feature list: operation_0524
feature list: operation_0525
feature list: operation 3730
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
software version: 2.9.6

FoPA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Script
application sub category: topic_0602
application sub category: topic 3407
application sub category: topic 3518
description: Formal model checking based pathway analysis (FoPA) - tool for identification of perturbed signaling pathways in clinical conditions using formal methods.
feature list: operation_0533
feature list: operation 3501
feature list: operation 3562
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: ReadMe.txt
primary contact: Mansoori F.

FoldamerDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 2828
application sub category: topic 3047
application sub category: topic 3068
application sub category: topic 3489
citation: GKZ993
citation: pubmed:31686102
description: The FoldamerDB is an open source database of foldamers. Foldamers are molecules which mimics the folding of biological molecules into well defined conformation
feature list: operation_0337
feature list: operation 2421
feature list: operation 2422
feature list: operation 3454
feature list: operation 3695
software help: help.php

FoodMicrobionet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 3297
application sub category: topic 3301
citation: j.ijfoodmicro.2015.12.001
citation: pubmed:26704067
description: Data resource collecting taxonomic composition and related metadata of > 2300 food and food-related samples. Data were produced according to a standardized pipeline and each sample is identified according the FoodEx2 classification (developed by the European Food Safety Authority to facilitate the comparison among different studies).
software version: 3.1

ForestQC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic 3168
application sub category: topic 3474
application sub category: topic 3518
citation: JOURNAL.PCBI.1007556
citation: pmcid:PMC6938691
citation: pubmed:31851693
description: Quality control on genetic variants from next-generation sequencing data using random forest. This classifier uses random forest model to identify good or bad variants from grey variants. $ conda install forestqc -c avallonking. To install the software. This software is compatible with OSX, 64-bit Linux and 64-bit Windows systems. If no HWE p-value file provided, HWE p-value would be computed by ForestQC. Or if ForestQC cannot find HWE p-value for some sites in the provided HWE p-value file, ForestQC would compute HWE p-value for those sites
feature list: operation_0452
feature list: operation 3196
feature list: operation 3225
feature list: operation 3675
feature list: operation 3695
license: MIT

FosSahul
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0621
application sub category: topic 3050
application sub category: topic 3489
citation: S41597-019-0267-3
citation: pmcid:PMC6864098
citation: pubmed:31745083
description: A database for the late quaternary fossil records of Sahul along with data processing scripts.

FossilJ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic 3077
application sub category: topic 3382
citation: PEERJ.PREPRINTS.27998V1
citation: PEERJ.PREPRINTS.27998V2
description: FossilJ is a ImageJ plugin for fossil data acquisition and semi-automatic measurements by image analysis.
feature list: operation 2409
feature list: operation 3435
feature list: operation 3443
license: GPL-3.0

Foundry
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0218
application sub category: topic_0749
application sub category: topic 3303
citation: bay130
citation: pmcid:PMC6301337
citation: pubmed:30576493
description: Message-oriented, horizontally scalable ETL system for scientific data integration and enhancement.
feature list: operation 2422
feature list: operation 3436
feature list: operation 3798
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
software help: README.md

FoxMask
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0610
application sub category: topic 3382
application sub category: topic 3500
citation: https://doi.org/10.1101/640037
description: Automated tool for animal detection in camera trap images.
feature list: operation 3891
is accessible for free: true
license: GPL-2.0
operating system: Linux
software help: https://foxmask.readthedocs.io/en/latest/
software help: README.rst
primary contact: Eric Devost

FractBias
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0780
citation: btw666
citation: pubmed:27794557
description: Graphical tool for assessing fractionation bias following polyploidy.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: FractBias
primary contact: Eric Lyons

FragBuilder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic_0593
application sub category: topic 2258
application sub category: topic 3314
citation: PEERJ.PREPRINTS.169V2
citation: peerj.277
citation: pmcid:PMC3961104
citation: pubmed:24688855
description: An efficient Python library to setup quantum chemistry calculations on peptides models. fragbuilder is a tool to create, setup and analyze QM calculations on peptides. FragBuilder will run with most versions of Open Babel, however there was bug in Open Babel which prevented some dihedral angles to be set accurately. If you experience this while using fragbuilder you will have to update your Open Babel
feature list: operation_0249
feature list: operation_0479
feature list: operation_0480
license: BSD-Source-Code
software help: fragbuilder-installation.html
software help: fragbuilder-setting-up-scan-of-peptide.html

FreeHi-C
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0654
application sub category: topic 3169
application sub category: topic 3174
application sub category: topic 3179
citation: s41592-019-0624-3
citation: pmcid:PMC8136837
citation: pubmed:31712779
description: FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation. FreeHi-C pipeline for high fidelity Hi-C data simulation. FreeHi-C: high fidelity Hi-C data simulation for benchmarking and data augmentation. FreeHi-C (v1.0) is short for Fragment interactions empirical estimation for fast simulation of Hi-C data. It is a data-driven Hi-C data simulator for simulating and augmenting Hi-C datasets. FreeHi-C employs a non-parametric strategy for estimating an interaction distribution of genome fragments and simulates Hi-C reads from interacting fragments. Data from FreeHi-C exhibit higher fidelity to the biological Hi-C data. FreeHi-C not only can be used to study and benchmark a wide range of Hi-C analysis methods but also boosts power and enables false discovery rate control for differential interaction detection algorithms through data augmentation
feature list: operation_0244
feature list: operation 3192
feature list: operation 3435
license: MIT

Frela
type: SoftwareApplication
input: UniProt accession
  type: FormalParameter
  additional type: data 3021
output: Z-value
  type: FormalParameter
  additional type: data 1668
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0091
citation: s41598-017-00465-5
citation: pmcid:PMC5428484
citation: pubmed:28336965
description: Frela is a web service for computing functional relationships of protein pairs based on Gene Ontology (GO) annotations. It allows very fast calculation of protein functional similarity based on their GO annotations for biological process (BP), molecular function (MF), and cellular component (CC) ontologies using various popular semantic similarity measures that can be combined arbitrarily with a set of widely used mixing strategies.
feature list: operation 1778
feature list: operation 3438
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: help

FrogCap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0194
application sub category: topic_0632
application sub category: topic 3168
application sub category: topic 3293
application sub category: topic 3512
citation: https://doi.org/10.1101/825307
description: FrogCap is a modular sequence capture probeset for phylogenomics and population genetics for frogs
feature list: operation 2419
feature list: operation 3192
feature list: operation 3196
primary contact: https://orcid.org/0000-0001-6381-6339

FullMeSH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3068
application sub category: topic 3382
application sub category: topic 3474
citation: btz756
citation: pmcid:PMC7523651
citation: pubmed:31596475
description: FullMeSH is a large-scale MeSH indexing method taking advantage of the recent increase in the availability of full text articles. The software is available upon request.
feature list: operation_0306
feature list: operation 3435
primary contact: Shanfeng Zhu

FunDMDeep-m6A
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 3295
application sub category: topic 3512
citation: BTZ316
citation: pmcid:PMC6612877
citation: pubmed:31510685
description: identification and prioritization of functional differential m6A methylation genes | A R package used to identify single base resolution m6A and differential m6A methylation site from MeRIP-seq data version 1.0
feature list: operation 3207
feature list: operation 3501

FunGeCo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0218
application sub category: topic_0602
application sub category: topic 3174
application sub category: topic 3697
citation: BTZ957
citation: pubmed:31882995
description: A web based tool for estimation of Functional potential of bacterial genomes and microbiomes using Gene Context information. Functional potential of bacterial genomes and microbiomes from gene context information. This feature allows the user to input a newly sequenced genome and annotate it using gene context based modules generated using extensive literature mining and manual curation. Users can also carry out comparative analysis (synteny view using parallel coordinates) of the uploaded genome with genomes already sequenced in NCBI using interactive visualizations. This feature allows comparison of functional modules in sequenced genomes obtained from NCBI. Users can interactively select upto five genomes which are compared using a synteny based visualization (parallel coordinates) and circular genomic representations. Information about individual modules in all these genomes can also be viewed as tabular outputs
feature list: operation_0306
feature list: operation_0362
feature list: operation 2495
feature list: operation 2939
feature list: operation 3208

FunMappOne
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic_0621
citation: s12859-019-2639-2
citation: pmcid:PMC6376640
citation: pubmed:30767762
description: User-friendly graphical interface that allows to visualize and summarize the functional annotations of one or multiple molecular biology experiments at once.
feature list: operation 2495
feature list: operation 3432
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: UserManual.999755866.pdf

FunVar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic_0769
citation: J.JBI.2019.103273
citation: pubmed:31454647
description: A systematic pipeline to unravel the convergence patterns of genetic variants in ASD | A Systematic Pipeline to Unravel the Convergence Patterns of Genetic Variants in Complex Diseases | FunVar (Functional annotation of Variants ) utilizes the existing resources to streamline and to improve the functional enrichment analysis of genetic variants disrupting genes in patients. FunVar, a semi-automated pipeline consist of three different and independent modules
feature list: operation 3501

Functional Heatmap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic 3308
application sub category: topic 3473
citation: s12859-019-2657-0
citation: pmcid:PMC6377781
citation: pubmed:30770734
description: Automated and interactive pattern recognition tool to integrate time with multi-omics assays.
feature list: operation_0531
feature list: operation 3501
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Daniel Watson
primary contact: Joshua Williams
primary contact: Ruoting Yang

Locating Retinal Blood Vessels on Fundus Images by Kirsch s Template and Fuzzy C-Means
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3344
application sub category: topic 3382
description: The code which segment the retinal blood vessels accurately. The Kirsch's template is used for tracking the larger blood vessels; fuzzy c-means is used to segment smaller blood vessels. The region based active contour method is used for edge detection and Morphoplogical operations are used to remove the background from the foreground fundus image. This methodology is suitable for different fundus image databases captured using different fundus cameras.
feature list: operation 3443
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: Jemima Jeba

Funmap2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0202
application sub category: topic_0625
citation: peerj.7008
citation: pmcid:PMC6546077
citation: pubmed:31183256
description: R package for QTL mapping using longitudinal phenotypes.
feature list: operation_0282
feature list: operation 3196
feature list: operation 3232
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Funmap2-manual.pdf
software help: Funmap2-vignette-v2.4.pdf
software version: 2.4.2
primary contact: N. Wang

FusionScan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: GI.2019.17.3.E26
citation: pmcid:PMC6808644
citation: pubmed:31610622
description: An accurate prediction of fusion genes from RNA-Seq data. Homepage may be broken as of January 4th, 2021.
feature list: operation 2454
feature list: operation 3192
feature list: operation 3359

G-Graph
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0622
application sub category: topic_0749
application sub category: topic 3382
author: Peter Andrews
citation: https://doi.org/10.1101/803015
description: An interactive genomic graph viewer. G-Graph is a free-software graphical desktop application that allows you to perform efficient exploratory analysis of genomic copy number and other numeric datasets. G-Graph can be installed and runs under the Linux, Mac, and Windows operating systems. G-Graph's features include the ability to easily zoom and scroll the view, alter the visual display properties, display gene annotations, link genes to the UCSC genome browser, and save application views to image and pdf format. G-Graph is also very fast and therefore supports smooth scrolling and zooming of views even for millions of data points
feature list: operation 2940
license: MIT

G-OnRamp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic 3170
application sub category: topic 3382
citation: btz309
citation: pmcid:PMC6821377
citation: pubmed:31070714
description: Galaxy-based platform for collaborative annotation of eukaryotic genomes.
feature list: operation_0525
feature list: operation 3208
feature list: operation 3216
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: training
software help: http://gonramp.wustl.edu/
primary contact: Jeremy Goecks
primary contact: Luke Sargent
primary contact: Sarah C.R. Elgin
primary contact: Wilson Leung

G-WIZ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 2885
application sub category: topic 3360
application sub category: topic 3517
citation: https://doi.org/10.1101/701086
citation: JOURNAL.PONE.0220215
citation: pmcid:PMC6894795
citation: pubmed:31805043
description: Assessing the performance of genome-wide association studies for predicting disease risk.
feature list: operation 3196
feature list: operation 3659
feature list: operation 3791

G2P
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 3517
citation: btz126
citation: pubmed:30848784
description: Genome-Wide-Association-Study simulation tool for genotype simulation, phenotype simulation and power evaluation.
feature list: operation_0282
feature list: operation 3196
feature list: operation 3557
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Xiaolei Liu

G3viz
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic 2640
citation: btz631
citation: pubmed:31393560
description: R package to interactively visualize genetic mutation data using a lollipop-diagram.
feature list: operation_0337
feature list: operation 3225
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: g3viz.pdf
primary contact: Xin Guo

GAD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Script
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic_0622
application sub category: topic_0780
application sub category: topic 3512
citation: https://doi.org/10.1101/815860
description: A Python script for dividing genome annotation files into feature-based files. A python script for extracting genome features from GTF/GFF3.
feature list: operation_0362
feature list: operation 2478
feature list: operation 3800

GADMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3056
description: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data

GAEseq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3474
citation: https://doi.org/10.1101/837674
citation: aaai.v34i01.5414
description: A Graph Auto-Encoder for Haplotype Assembly and Viral Quasispecies Reconstruction.
feature list: operation_0310
feature list: operation_0484
feature list: operation_0487
feature list: operation 3198
feature list: operation 3211

GAG builder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0602
application sub category: topic 3520
citation: gky1035
citation: pmcid:PMC6324007
citation: pubmed:30371822
description: Online tool to build 3D models of GAG sequences from GlycoCT codes.
feature list: operation 2422
feature list: operation 3561
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Builder.pdf

Genome Annotator Light (GAL)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0622
application sub category: topic_0780
citation: j.ygeno.2019.03.012
citation: pubmed:30926570
description: A Docker-based package for genome analysis and visualization.
feature list: operation_0362
feature list: operation 3208
feature list: operation 3216
is accessible for free: true
operating system: Linux
software help: GAL
software help: User Guide Latest.pdf
software version: 1.1
primary contact: Arijit Panda

GAMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic 2269
application sub category: topic 3305
application sub category: topic 3524
citation: s10707-018-00339-6
citation: PEERJ.PREPRINTS.2231V2
description: GAMA is a modeling and simulation development environment for building spatially explicit agent-based simulations.
feature list: operation 2426
operating system: Linux
operating system: Mac
operating system: Windows
software help: Tutorials

GAMer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2828
application sub category: topic 3306
application sub category: topic 3452
citation: https://doi.org/10.1101/765453
description: An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries | Geometry-preserving Adaptive Mesher | GAMer is a surface mesh improvement library developed to condition surface meshes derived from noisy biological imaging data. Using Tetgen, GAMer can generate tetrahedral meshes suitable for finite elements simulations of reaction-diffusion systems among others. GAMer has the following main features: | Geometry-preserving Adaptive Mesher — GAMer v2.0.5 documentation | Free document hosting provided by Read the Docs
license: LGPL-2.1
software help: gamer.readthedocs.io

GAPPA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0637
application sub category: topic 3174
application sub category: topic 3293
citation: https://doi.org/10.1101/647958
description: Collection of commands for working with phylogenetic data.
feature list: operation_0325
feature list: operation_0567
feature list: operation 3478
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md

GASAL2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0080
application sub category: topic_0097
application sub category: topic_0099
application sub category: topic_0654
application sub category: topic 3168
citation: s12859-019-3086-9
citation: s12859-019-3185-7
citation: pmcid:PMC6815017
citation: pmcid:PMC6862790
citation: pubmed:31653208
citation: pubmed:31744474
description: a GPU accelerated sequence alignment library for high-throughput NGS data. GASAL2 - GPU-accelerated DNA alignment library. GASAL2 is an easy-to-use CUDA library for DNA/RNA sequence alignment algorithms. Currently it supports different kind of alignments:. A Linux platform with CUDA toolkit 8 or higher is required, along with usual build environment for C and C++ code. GASAL2 has been tested over NVIDIA GPUs with compute capabilities of 2.0, 3.5 and 5.0. Although lower versions of the CUDA framework might work, they have not been tested
feature list: operation_0491
feature list: operation_0495
feature list: operation_0496
license: Apache-2.0

GATK PathSeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3308
application sub category: topic 3673
citation: bty501
citation: pmcid:PMC6289130
citation: pubmed:29982281
description: Customizable computational tool included in Genome Analysis Toolkit (GATK) for the discovery and identification of microbial sequences in libraries from eukaryotic hosts.
feature list: operation 3192
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Matthew Meyerson

GBIF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0637
application sub category: topic_0780
application sub category: topic 3050
application sub category: topic 3277
application sub category: topic 3303
citation: PHYTOKEYS.133.37481
citation: pmcid:PMC6805691
citation: pubmed:31656398
description: GBIF—the Global Biodiversity Information Facility—is an international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.
feature list: operation 2421
software help: GBIF.ES Inf Col 2014.pdf

GBOL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Ontology
application sub category: topic_0089
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic 2229
citation: S41597-019-0263-7
citation: pmcid:PMC6828702
citation: pubmed:31685817
description: The Empusa code generator and its application to GBOL. GBOL; Genome Biology Ontology Language. To enable interoperability of genome annotations, we have developed the Genome Biology Ontology Language (GBOL) and associated stack (GBOL stack). A group is a collection of several projects. If you organize your projects under a group, it works like a folder.
feature list: operation_0224
feature list: operation_0362
feature list: operation 3559

GBS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic 3518
application sub category: topic 3673
citation: S12864-019-5998-1
citation: pmcid:PMC6683502
citation: pubmed:31387530
description: Screening populations for copy number variation using genotyping-by-sequencing | Detection of deletions and duplications from GBS data | delgbs is an R package which provides tools for detecting copy number variation from genotyping-by-sequencing (GBS) data. delgbs bases its CNV calls on the number of reads per sample in discrete bins (e.g. 1-kb bins) located along a reference genome
feature list: operation_0452
feature list: operation 3196
feature list: operation 3798
license: GPL-3.0

GCAC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic 2258
application sub category: topic 3336
application sub category: topic 3379
citation: s12859-018-2492-8
citation: pmcid:PMC7394323
citation: pubmed:30717669
description: Galaxy workflow system for predictive model building for virtual screening.
feature list: operation_0482
feature list: operation 2428
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: gcac-galaxy-tools
primary contact: Andrew M. Lynn

GCMDR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic 3375
application sub category: topic 3518
citation: BTZ621
citation: pubmed:31397851
description: Graph convolution for predicting associations between miRNA and drug resistance | IMPLEMENT FOR graph convolution for predicting associations between miRNA and drug resistance using raw data
feature list: operation_0463
feature list: operation 3482
feature list: operation 3792

GCNG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3474
citation: https://doi.org/10.1101/2019.12.23.887133
description: Graph convolutional networks for inferring cell-cell interactions. using graph convolutional neural network and spaital transcriptomics data to infer cell-cell interactions. GCNG for extracellular gene relationship inference. (A) GCNG model using spatial single cell expression data
feature list: operation 2436
feature list: operation 3439
feature list: operation 3625

GCPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0154
application sub category: topic_0749
application sub category: topic_0780
citation: bty067
citation: pubmed:29420675
description: Web tool for guanylyl cyclase functional centre prediction from amino acid sequence.
feature list: operation_0418
feature list: operation_0478
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Aloysius Wong

GEAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic_0780
application sub category: topic 3168
citation: FGENE.2019.01046
citation: pmcid:PMC6902276
citation: pubmed:31850053
description: Complement Genome Annotation Lift Over Using a Weighted Sequence Alignment Strategy. This toolkit deals with GEnomic sequence and genome structure ANnotation files between inbreeding lines and species. The gene sequence and genetic feature variation between different individuals are very important for natural variation research
feature list: operation_0292
feature list: operation_0362
feature list: operation_0524
feature list: operation 3227
feature list: operation 3644
license: MIT

GEAR-base
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0196
application sub category: topic_0625
application sub category: topic 3168
citation: J.GPB.2018.11.002
citation: pmcid:PMC6624217
citation: pubmed:31100356
description: GEnetic Antibiotic Resistance and Susceptibility Database.
feature list: operation 3196
feature list: operation 3482
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
primary contact: Andreas E. Posch
primary contact: Andreas Keller

GEDFN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3360
application sub category: topic 3474
application sub category: topic 3697
citation: FGENE.2019.01182
citation: pmcid:PMC6883002
citation: pubmed:31824573
description: Graph Embedding Deep Learning Guides Microbial Biomarkers' Identification. graph embedding deep learning guide microbial biomarkers' identification.
feature list: operation 2940
feature list: operation 3439

GEDIT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3518
citation: https://doi.org/10.1101/728493
description: Accurate Cell Type Quantification from Gene Expression Data | Abstract The cell type composition of heterogeneous tissue samples can be a critical variable in both clinical and laboratory settings. However, current experimental methods of cell type quantification (e.g. cell flow cytometry) are costly, time consuming and can introduce bias. Computational approaches that infer cell type abundance from expression data offer an alternate solution. While these methods have gained popularity, most are limited to predicting hematopoietic cell types and do not produce accurate predictions for stromal cell types. Many are also limited to particular platforms, whether RNA-Seq or specific microarray models. To overcome these limitations, we present the Gene Expression Deconvolution Interactive Tool, or GEDIT. Using simulated and experimental data, we demonstrate that GEDIT produces accurate results for both stromal and hematopoietic cell types
feature list: operation 2495
feature list: operation 3629
feature list: operation 3800

GEM-NET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3303
application sub category: topic 3314
application sub category: topic 3489
citation: ACSCENTSCI.9B00111
citation: pmcid:PMC6661976
citation: pubmed:31404233
description: Lessons in Multi-Institution Teamwork Using Collaboration Software | Dashboard to view/download files from segregated Google Shared Drives | Center for Genetically Encoded Materials (C-GEM) | GEM-NET is the home of the Center for Genetically Encoded Materials (C-GEM), an NSF CCI (Center for Chemical Innovation) | Center for Genetically Encoded Materials | C-GEM seeks to establish a fundamentally new way to program chemical matter and transform the way we produce materials and medicines

GEMME
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic 3303
application sub category: topic 3398
citation: MSZ179
citation: pmcid:PMC6805226
citation: pubmed:31406981
description: a simple and fast global epistatic model predicting mutational effects | The systematic and accurate description of protein mutational landscapes is a question of utmost importance in biology, bioengineering and medicine. Recent progress has been achieved by leveraging on the increasing wealth of genomic data and by modelling inter-site dependencies within biological sequences. However, state-of-the-art methods remain time consuming. Here, we present GEMME (www.lcqb.upmc.fr GEMME), an original and fast method that predicts mutational outcomes by explicitly modelling the evolutionary history of natural sequences. This allows accounting for all positions in a sequence when estimating the effect of a given mutation. GEMME uses only a few biologically meaningful and interpretable parameters. Assessed against 50 high- and low-throughput mutational experiments, it overall performs similarly or better than existing methods
feature list: operation_0331

GEMMER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3382
citation: bty052
citation: pmcid:PMC9881680
citation: pubmed:29401212
description: GEMMER (GEnome-wide tool for Multi-scale Modeling data Extraction and Representation), a web-based data-integration tool that facilitates high quality visualization of physical, regulatory and genetic interactions between proteins/genes in Saccharomyces cerevisiae.
feature list: operation 2422
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: http://gemmer.barberislab.com/index.php
primary contact: Matteo Barberis

GEMtractor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0821
application sub category: topic 3382
application sub category: topic 3407
citation: https://doi.org/10.1101/790725
description: Extracting Views into Genome-scale Metabolic Models. The GEMtractor a platform for trimming and extracting genome-scale metabolic models (GEMs).
feature list: operation 3192
feature list: operation 3280
feature list: operation 3660
license: GPL-3.0

GENAVi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3170
citation: S12864-019-6073-7
citation: pmcid:PMC6796420
citation: pubmed:31619158
description: a shiny web application for gene expression normalization, analysis and visualization. GENAVi (Gene Expression Normalization Analysis and Visualization) is an rshiny web application that provides a GUI based platform for the analysis of gene expression data. GENAVi combines several R packages commonly used for normalizing, clustering, visualizing, and performing differential expression analysis (DEA) on RNA-seq data
feature list: operation_0571
feature list: operation 2436
feature list: operation 2939
feature list: operation 3435
feature list: operation 3891

GENCODE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0622
application sub category: topic_0659
application sub category: topic_0769
citation: gkaa1087
citation: gky955
citation: gr.132159.111
citation: gr.135350.111
citation: pmcid:PMC3431492
citation: pmcid:PMC3431493
citation: pmcid:PMC6323946
citation: pmcid:PMC7778937
citation: pubmed:22955987
citation: pubmed:22955988
citation: pubmed:30357393
citation: pubmed:33270111
description: Consortium identifying and classifying all gene features in the human and mouse genomes with high accuracy based on biological evidence, and releasing these annotations for the benefit of biomedical research and genome interpretation.
feature list: operation 2422
feature list: operation 3501
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: biotypes.html
software help: custom array.html
software help: data access.html
software help: data format.html
software help: faq.html
software help: rgasp
software help: tags.html

GENOMICUS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0194
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic_0623
application sub category: topic_0797
application sub category: topic 3299
application sub category: topic 3943
citation: btq079
citation: gkab1091
citation: gks1156
citation: gku1112
citation: gkx1003
description: Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
feature list: operation_0224
feature list: operation_0292
feature list: operation_0490
feature list: operation_0567
feature list: operation 3208
is accessible for free: true
software help: https://www.youtube.com/watch
primary contact: http://orcid.org/0000-0001-7032-5650
primary contact: 0000-0002-8209-173X

GEO2RNAseq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: https://doi.org/10.1101/771063
description: An easy-to-use R pipeline for complete pre-processing of RNA-seq data | You're trying to access a page that requires authentication. × | Home: https://bitbucket.org/thomas_wolf/geo2rnaseq/overview | RNA-seq is a method that uses next-generation sequencing to quantify and analyze RNA. It can be used for finding significantly differentially expressed genes (DEGs) in well sequenced organisms. This package is a complete function library for analyzing read files, trimming of raw reads, mapping on reference genomes, counting reads per gene and finding significant DEGs | PRIVACY POLICY : EULA (Anaconda Cloud v2.33.29) © 2019 Anaconda, Inc. All Rights Reserved | Follow us on Twitter Tap To Close Find us on Facebook Tap To Close Follow us on Slideshare Tap To Close Find us on LinkedIn Tap To Close Follow us on Instagram Tap To Close Watch us on YouTube Tap To Close Follow us on GitHub Tap To Close
feature list: operation 3192
feature list: operation 3223
feature list: operation 3435
software help: overview

GEREDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0091
application sub category: topic_0204
application sub category: topic_0218
application sub category: topic_0219
citation: S0219720019500240
citation: pubmed:31617460
description: Gene expression regulation database curated by mining abstracts from literature. Gene Expression Regulation Database. Gene Expression Regulation Database (GREDB) has been developed to facilitate systems-level analyses that will provide insights into the question of how genes are regulated that governing a specific biological response. GREDB is a publicly available, manually curated biological database depositing the human gene expression regulation relationships (Links). To date, more than 39,000 Links have been contextual-ly annotated through the review of 53,000 plus abstracts. GREDB has the ability to analyze user-supplied gene expression data using the GEREA bioinformatics tool in a causal analysis oriented manner. The database can be searched use NCBI official gene symbol (eg. CDC42). The new version of GereDB is online for testing, please visit the following link: Run New GereDB online. Huang, Tinghua & Huang, Xiali & Shi, Bomei & Yao, Min. (2019)
feature list: operation_0306
feature list: operation 2421
feature list: operation 2495
feature list: operation 3431

GERONIMO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0080
application sub category: topic 3293
application sub category: topic 3299
author: Agata Kilar
description: GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Windows
software help: GERONIMO.git
software version: 1.0

GESUR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0736
application sub category: topic 2640
application sub category: topic 3170
citation: J.JGG.2019.08.003
citation: pubmed:31630971
description: Identification of transcriptional isoforms associated with survival in cancer patient. GESUR performs overall survival (OS) or disease free survival (DFS, also called relapse-free survival and RFS) analysis based on expression of a gene set. GESUR uses Log-rank test, a.k.a the Mantel–Cox test, for hypothesis test. Cohorts thresholds can be adjusted, and gene-pairs can be used. The cox proportional hazard ratio and the 95% confidence interval information can also be included in the survival plot.
feature list: operation_0264
feature list: operation 2238
feature list: operation 2495

GET-IT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0610
application sub category: topic 3361
application sub category: topic 3489
citation: PEERJ.PREPRINTS.2233V2
description: Exploiting observations and measurement data standard for distributed LTER-Italy freshwater sites. Water quality issues. Geoinformation Enabling ToolkIT starterkit. Geoinformation Enabling ToolkIT starterkit ®. GET-IT allows you to easily share geospatial data on the web with simple actions. Share your maps, measurements, and sensors.
feature list: operation 2422
feature list: operation 3435

GE LDA Survival
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3421
application sub category: topic 3474
application sub category: topic 3518
citation: JOURNAL.PONE.0224446
citation: pmcid:PMC6857918
citation: pubmed:31730620
description: Gene expression based survival prediction for cancer patients. Gene Expression based Survival Prediction for Cancer Patients – A Topic Modeling Approach. This repository includes source code from the publication Gene Expression based Survival Prediction for Cancer Patients – A Topic Modeling Approach. You can find the code for the MTLR algorithm here http://pssp.srv.ualberta.ca/home/about.
feature list: operation_0571
feature list: operation 2454
feature list: operation 3891

GFA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3295
application sub category: topic 3474
application sub category: topic 3517
citation: https://doi.org/10.1101/2019.12.19.19015347
description: An integrative machine learning approach to discovering multi-level molecular mechanisms of obesity using data from monozygotic twin pairs. We combined clinical, cytokine, genomic, methylation and dietary data from 43 young adult monozygotic twin pairs (aged 22 36, 53% female), where 25 of the twin pairs were substantially weight discordant (delta BMI > 3kg m2). These measurements were originally taken as part of the TwinFat study, a substudy of The Finnish Twin Cohort study. These five large multivariate data sets (comprising 42, 71, 1587, 1605 and 63 variables, respectively) were jointly analysed using an integrative machine learning method called Group Factor Analysis (GFA) to offer new hypotheses into the multi-molecular-level interactions associated with the development of obesity. New potential links between cytokines and weight gain are identified, as well as associations between dietary, inflammatory and epigenetic factors
feature list: operation 3659
feature list: operation 3891

GGMs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic 2269
application sub category: topic 3172
citation: btz357
citation: pmcid:PMC6901079
citation: pubmed:31077287
description: Exact hypothesis testing for shrinkage based Gaussian Graphical Models.
feature list: operation 2238
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Peter Horvatovich

GIDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0218
application sub category: topic_0659
application sub category: topic 2640
citation: BAZ051
citation: pmcid:PMC6517830
citation: pubmed:31089686
description: Knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal (GI) cancer.
feature list: operation_0306
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.htmlq
primary contact: Xiaoyan Zhang
primary contact: Ying Wang

GISA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0736
application sub category: topic 3315
citation: https://doi.org/10.1101/758029
description: Using Gauss Integrals to identify rare conformations in protein structures | Abstract The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots, slipknots, lassos, links, and pokes, and with each method aimed only for a specific set of such configurations. We here propose a general method which transforms a structure into a “fingerprint of topological-geometric values” consisting in a series of real-valued descriptors from mathematical Knot Theory. The extent to which a structure contains unusual configurations can then be judged from this fingerprint. The method is therefore not confined to a particular pre-defined topology or geometry (like a knot or a poke), and so, unlike existing methods, it is general

GITAR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0602
application sub category: topic_0769
application sub category: topic 3656
citation: j.gpb.2018.06.006
citation: pmcid:PMC6364044
citation: pubmed:30553884
description: GITAR (Genome Interaction Tools and Resources) is a standardized, easy to use and flexible solution to manage Hi-C genomic interaction data, from processing to storage and visualization, composed of two modules: HiCtool and a processed data library.
feature list: operation 1812
feature list: operation 3501
feature list: operation 3798
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: ReadMe.md

GL-UVAB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0194
application sub category: topic_0621
application sub category: topic_0781
application sub category: topic 3050
application sub category: topic 3174
citation: S12915-019-0723-8
citation: pmcid:PMC6936153
citation: pubmed:31884971
description: Charting the diversity of uncultured viruses of Archaea and Bacteria. Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. Perl script that automates the analyses to establish GL-UVAB (Genomic Lineages of Uncultured Viruses of Archaea and Bacteria). These include: 1) Identification of protein encoding genes with Prodigal. 2) All-versus-all protein search with Diamond. 3) Calculating Dice distances. 4) Building Dice tree using R 5) Identifying lineages based on the user defined criteria
feature list: operation_0362
feature list: operation 3198
feature list: operation 3460

GLAMbox
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 2269
application sub category: topic 3304
citation: https://doi.org/10.1101/741678
citation: journal.pone.0226428
citation: pmcid:PMC6914332
citation: pubmed:31841564
description: A Python toolbox for investigating the association between gaze allocation and decision behaviour | A python toolbox for the Gaze Weighted Linear Accumulator Model (GLAM) | GLAMbox is a Python toolbox for investigating the association between gaze allocation and decision behaviour, and applying the Gaze-weighted Linear Accumulator Model (Thomas, Molter et al., 2019, full text available online)
feature list: operation 3436
license: MIT

GLANET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0749
application sub category: topic 3168
application sub category: topic 3173
citation: btx326
citation: pmcid:PMC6355098
citation: pubmed:28541490
description: Genomic loci annotation and enrichment tool.
feature list: operation 3197
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest
primary contact: Burçak Otlu

GLM-PCA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 3170
citation: S13059-019-1861-6
citation: pmcid:PMC6927135
citation: pubmed:31870412
description: Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model. Dimension Reduction of Non-Normally Distributed Data. Implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed data such as counts or binary matrices.
feature list: operation 2939
feature list: operation 3563
feature list: operation 3891
license: Artistic-2.0

GLOSSary
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0099
application sub category: topic 3174
citation: s12859-018-2423-8
citation: pmcid:PMC6266928
citation: pubmed:30497362
description: 16S subunit related sequences database, identified from metagenomic efforts as part of the Tara Oceans project. It includes a BLAST search tool. The analysis system incorporates the SILVA collection, allowing comparative analyses to identify unclassified sequences and their geographical distribution.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: GLOSSary USER GUIDE.pdf

GLUE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic_0781
application sub category: topic 3305
citation: s12859-018-2459-9
citation: pmcid:PMC6299651
citation: pubmed:30563445
description: GLUE (Genes Linked by Underlying Evolution) is data-centric bioinformatics environment for virus sequence data, with a focus on variation, evolution and sequence interpretation.
feature list: operation_0499
feature list: operation_0564
feature list: operation 3196
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
primary contact: Josh Singer
primary contact: Robert Gifford

GLycan Array Dashboard
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic 3068
application sub category: topic 3518
citation: btz075
description: Web-based tool to visualize, analyze, present and mine glycan microarray data.
feature list: operation 1812
feature list: operation 3218
feature list: operation 3802
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation
software version: 2.0

GMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3517
citation: BTZ304
citation: pubmed:31070732
description: Efficient Multivariate Analysis Algorithms for Longitudinal Genome-wide Association Studies.
feature list: operation_0282
feature list: operation 3196
feature list: operation 3659
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: User Manual for GMA 2019.4.20.pdf
primary contact: Jian-Feng Liu

GMCLDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 2640
citation: JBHI.2019.2958389
citation: pubmed:31825885
description: Predicting human lncRNA-disease associations based on geometric matrix completion. Recently, increasing evidences have indicated that dysregulations of long non-coding RNAs (lncRNAs) are implicated in various complex diseases. However, only a limited number of lncRNA-disease associations are experimentally verified. Prioritizing potential lncRNA-disease associations is beneficial not only for understanding disease mechanisms at lncRNA level, but also for disease diagnosis. Various computational methods have been proposed, but precise prediction and full use of data's intrinsic structure are still challenging. In this study, we propose a new method, named GMCLDA (Geometric Matrix Completion lncRNA-Disease Association), to infer potential lncRNA-disease associations based on geometric matrix completion.
feature list: operation_0346

GMpi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0780
application sub category: topic 3385
application sub category: topic 3810
citation: APS3.11280
citation: pmcid:PMC6711351
citation: pubmed:31467803
description: Affordable remote monitoring of plant growth in facilities using Raspberry Pi computers | A growth chamber sensing system using the Raspberry Pi as a platform | GMpi: A Growth Chamber Monitoring System Using the Raspberry Pi as a Platform | The GMpi is a cost-effective solution for monitoring the conditions of a growth chamber, greenhouse, or any other facility for which specific conditions (temperature, light, humidity, etc.) need to be maintained

GMrepo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0219
application sub category: topic_0625
application sub category: topic 3174
citation: GKZ764
citation: pubmed:31504765
description: a database of curated and consistently annotated human gut metagenomes | GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and accessibility of the rapidly growing human metagenomic data. This is achieved by consistently annotating the microbial contents of collected samples using state-of-art toolsets and by manual curation of the meta-data of the corresponding human hosts. GMrepo organizes the collected samples according to their associated phenotypes and includes all possible related meta-data such as age, sex, country, body-mass-index (BMI) and recent antibiotics usage. To make relevant information easier to access, GMrepo is equipped with a graphical query builder, enabling users to make customized, complex and biologically relevant queries
feature list: operation_0362

GO2Vec
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0128
application sub category: topic_0621
application sub category: topic 3474
citation: s12864-019-6272-2
citation: pmcid:PMC8424702
citation: pubmed:31874639
description: transforming GO terms and proteins to vector representations via graph embeddings. BACKGROUND:Semantic similarity between Gene Ontology (GO) terms is a fundamental measure for many bioinformatics applications, such as determining functional similarity between genes or proteins. Most previous research exploited information content to estimate the semantic similarity between GO terms; recently some research exploited word embeddings to learn vector representations for GO terms from a large-scale corpus. In this paper, we proposed a novel method, named GO2Vec, that exploits graph embeddings to learn vector representations for GO terms from GO graph. GO2Vec combines the information from both GO graph and GO annotations, and its learned vectors can be applied to a variety of bioinformatics applications, such as calculating functional similarity between proteins and predicting protein-protein interactions
feature list: operation 2492
feature list: operation 3435
license: GPL-3.0

GOMAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0089
application sub category: topic_0196
application sub category: topic_0622
application sub category: topic_0780
application sub category: topic 3316
citation: https://doi.org/10.1101/809988
description: Gene Ontology Meta Annotator for Plants. Lawrence-Dill Plant Informatics and Computation Lab. Welcome to GOMAP-singularity’s documentation! — GOMAP-Singularity 1.3.2 documentation. All publications and products by the team at Lawrence-Dill Plant Informatics and Computation Lab. Click on the link to learn more. Publicly available GOMAP Datasets. These datasets generated by GOMAP are new high-coverage and reproducible functional annotation sets of protein coding genes based on Gene Ontology (GO) term assignments. Follow the DOI link for more information, access, and download. Check out the main project page (Home on the left) to find out more about how they were generated and how you can use the pipeline yourself.
feature list: operation_0310
feature list: operation_0362
feature list: operation 3672
software help: latest

GOPHER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0204
application sub category: topic_0632
application sub category: topic_0749
citation: s12864-018-5376-4
citation: pmcid:PMC6332836
citation: pubmed:30642251
description: Generator of probes for capture Hi-C experiments at high resolution.
feature list: operation_0309
feature list: operation 3501
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: latest
primary contact: The Jackson Laboratory

GOT-10k
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic 3382
application sub category: topic 3474
application sub category: topic 3489
citation: TPAMI.2019.2957464
citation: pubmed:31804928
description: A Large High-Diversity Benchmark for Generic Object Tracking in the Wild. Generic Object Tracking Benchmark. A large, high-diversity, one-shot database for generic object tracking in the wild
feature list: operation 3436

GOTrapper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0089
application sub category: topic_0203
application sub category: topic 3518
citation: s12859-018-2581-8
citation: pmcid:PMC6330489
citation: pubmed:30634902
description: Tool to navigate through branches of gene ontology hierarchy.
feature list: operation 2422
feature list: operation 2495
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Hezha Hassan

GOcats
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0102
application sub category: topic 3518
citation: JOURNAL.PONE.0220728
citation: pmcid:PMC6695228
citation: pubmed:31415589
description: Advances in gene ontology utilization improve statistical power of annotation enrichment | Welcome to GOcats’ documentation! — GOcats 1.1.5 documentation
feature list: operation 3352
feature list: operation 3501
feature list: operation 3559

GOnet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0121
application sub category: topic_0602
citation: s12859-018-2533-3
citation: pmcid:PMC6286514
citation: pubmed:30526489
description: Tool for interactive Gene Ontology analysis.
feature list: operation 2422
feature list: operation 3501
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: index
primary contact: Mikhail Pomaznoy

GPCRmd
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic_0209
application sub category: topic_0593
application sub category: topic_0820
application sub category: topic 3892
citation: https://doi.org/10.1101/839597
description: GPCRmd uncovers the dynamics of the 3D-GPCRome. The online resource for GPCR simulations. GPCRmd is an online platform with web-based visualization capabilities and a comprehensive analysis toolbox that allows scientists from any discipline to visualize, inspect, and analyse GPCR molecular dynamics.
feature list: operation_0269
feature list: operation 2476
feature list: operation 2995
feature list: operation 3891

GPI-anchor biosynthesis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3334
citation: MGG3.743
citation: pmcid:PMC6625143
citation: pubmed:31127708
description: Inherited glycophosphatidylinositol deficiency variant database.
feature list: operation_0417
feature list: operation 3225
feature list: operation 3431
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0001-9713-7107

GPRED-GC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0114
application sub category: topic_0622
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3500
citation: S12859-019-3047-3
citation: pmcid:PMC6929509
citation: pubmed:31874598
description: a Gene PREDiction model accounting for 5 '- 3' GC gradient. a Gene PREDiction model accounting for 5'-3' GC gradient. A new hidden Markov model (HMM)-based ab initio. gene prediction tool for finding genes with highly variable GC contents such as the genes with negative GC gradients in grass genomes.
feature list: operation_0430
feature list: operation_0476
feature list: operation 2454

GPSRdocker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic 2259
application sub category: topic 3068
citation: https://doi.org/10.1101/827766
description: A Docker-based Resource for Genomics, Proteomics and Systems biology. Welcome to GPSRdocker A resource for Genomics, Proteomics and Systems biology. GPSRdocker is a docker-based container that provides a resources on Genomics, Proteomics and System Biology
feature list: operation_0267
feature list: operation 2489
feature list: operation 3461

GPUAM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3314
citation: ACS.JCIM.8B00951
citation: pubmed:31145605
description: Implementation of the Molecular Electrostatic Potential over Graphics Processing Units.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: GPUAM manual.pdf
software help: README.md
primary contact: Jorge Garza

GPress
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3676
citation: https://doi.org/10.1101/833087
description: A framework for querying General Feature Format (GFF) files and feature expression files in a compressed form”. This is the GPress, a framework for querying GTF, GFF3 and expression files in a compressed form. Here, we will use the test files to provide an example of how to use GPress. We will use GTF file for illustration since the GFF3 file is nearly the same except slight format variations. We will store the compressed GTF file and compressed expression file in a new folder gtf1
feature list: operation_0335
feature list: operation 1812
feature list: operation 2421
feature list: operation 2422
feature list: operation 3802

GPseudoClust
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3518
citation: btz778
citation: pmcid:PMC7703763
citation: pubmed:31608923
description: deconvolution of shared pseudo-profiles at single-cell resolution. Code for the GPseudoClust method, including pre- and postprocessing steps. Magdalena E Strauß, Paul DW Kirk, John E Reid, Lorenz Wernisch (2019); GPseudoClust: deconvolution of shared pseudo-trajectories at single-cell resolution
feature list: operation_0313
feature list: operation_0337
feature list: operation 3629
license: GPL-3.0

GRAM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3295
citation: JOURNAL.PGEN.1007860
citation: pmcid:PMC6742416
citation: pubmed:31469829
description: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner | GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell type-specific manner
feature list: operation_0331
feature list: operation_0441
feature list: operation 3232

GRANAR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web application
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3067
citation: https://doi.org/10.1101/645036
description: Generator of Root ANAtomy in R (GRANAR) is a new open-source computational tool that can be used to rapidly generate digital versions of root anatomical networks.
feature list: operation 3891
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Guillaume Lobet

GRANVIL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3168
citation: 1753-6561-5-S9-S107
citation: pmcid:PMC3287830
citation: pubmed:22373025
description: GRANVIL (Gene- or Region-based ANalysis of Variants of Intermediate and Low frequency) - performs rare-variant analysis of binary or quantitative phenotypes. The method is based on accumulation of minor alleles of rare or uncommon markers discovered through dense genotyping or resequencing data. Association analyses are based on gene- or other pre-defined regions, determined by analyst.
feature list: operation 1812
feature list: operation 3196
feature list: operation 3791
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

GRASE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: MSYSTEMS.00384-19
citation: pmcid:PMC6749106
citation: pubmed:31530648
description: Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes | Genome Relative Abundance to Sequencing Effort: a tool for planning MAG sequencing experiments | grase is a package that estimates the sequencing effort required to achieve a goal of MAG construction. This is based on a model presented in Royalty and Steen (2018)
feature list: operation_0310
feature list: operation_0362
feature list: operation 3798

GRASS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic 3382
citation: PEERJ.PREPRINTS.2253V2
description: From photo-geology to 3D geological models. An open source approach. GRASS GIS is a free Geographic Information System (GIS) software used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization.
feature list: operation 3431

GREIN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3518
citation: S41598-019-43935-8
citation: pmcid:PMC6527554
citation: pubmed:31110304
description: Interactive Web Platform for Re-analyzing Gene Expression Omnibus (GEO) RNA-seq Data.
feature list: operation 2495
feature list: operation 3223
feature list: operation 3431
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: http://www.ilincs.org/apps/grein/
primary contact: https://orcid.org/0000-0003-4510-3102

GRIBCG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0654
application sub category: topic_0780
application sub category: topic 3500
citation: s12859-019-2712-x
citation: pmcid:PMC6416924
citation: pubmed:30866794
description: Guide RNA Identifier for Balancer Chromosome Generation (GRIBCG) - software for selection of sgRNAs in the design of balancer chromosomes.
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: B. Merritt

GRN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 2640
citation: https://doi.org/10.1101/735514
description: Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms | Abstract The gene regulatory network (GRN) of human cells encodes mechanisms to ensure proper functioning. However, if this GRN is dysregulated, the cell may enter into a disease state such as cancer. Understanding the GRN as a system can therefore help identify novel mechanisms underlying disease, which can lead to new therapies. Reliable inference of GRNs is however still a major challenge in systems biology. To deduce regulatory interactions relevant to cancer, we applied a recent computational inference framework to data from perturbation experiments in squamous carcinoma cell line A431. GRNs were inferred using several methods, and the false discovery rate was controlled by the NestBoot framework. We developed a novel approach to assess the predictiveness of inferred GRNs against validation data, despite the lack of a gold standard
feature list: operation_0277
feature list: operation 1781
feature list: operation 3439

GRO2LAM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0176
application sub category: topic_0749
application sub category: topic 3368
citation: S00894-019-4011-X
citation: pubmed:31065808
description: GROMACS to LAMMPS (GRO2LAM) - converter for molecular dynamics software.
feature list: operation 2476
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

GRONS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3068
application sub category: topic 3295
citation: BAX097
citation: pmcid:PMC5750854
citation: pubmed:31725863
description: A comprehensive genetic resource of nicotine and smoking. Genetic resources of nicotine and smoking. Genetic Resources Of Nicotine and Smoking (GRONS) is a database devoted to provide a comprehensive and systematic collection of cross-platform genetic data on genes associated with the biological response to nicotine exposure and smoking related behaviors or diseases. By this database, we try to make such information easily accessible and interpretable for investigators in the smoking/nicotine addiction research community
feature list: operation_0283
feature list: operation_0305
feature list: operation 3196
feature list: operation 3431

GRaMM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0634
application sub category: topic 3172
application sub category: topic 3300
application sub category: topic 3697
citation: ACS.ANALCHEM.9B02948
citation: pubmed:31638380
description: Strategy for Intercorrelation Identification between Metabolome and Microbiome. Accumulating evidence points to the strong and complicated associations between the metabolome and the microbiome, which play diverse roles in physiology and pathology. Various correlation analysis approaches were applied to identify microbe-metabolite associations. Given the strengths and weaknesses of the existing methods and considering the characteristics of different types of omics data, we designed a special strategy, called Generalized coRrelation analysis for Metabolome and Microbiome (GRaMM), for the intercorrelation discovery between the metabolome and microbiome.
feature list: operation 2940
feature list: operation 3463
feature list: operation 3659
feature list: operation 3891
license: GPL-3.0

GSAn
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic_0625
citation: https://doi.org/10.1101/648444
description: Gene Set Annotation - an alternative to enrichment analysis for annotating gene sets.
feature list: operation 2942
feature list: operation 3196
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Mac
operating system: Windows
software help: documentation

GSSO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0634
application sub category: topic 3410
citation: SHTI190213
citation: pubmed:31437915
description: The Gender, Sex, and Sexual Orientation (GSSO) Ontology | GSSO is the Gender, Sex, and Sex Orientation ontology, including terms related to gender identity and expression, sexual and romantic identity and orientation, and sexual and reproductive behavior | Gender, Sex, and Sexual Orientation
feature list: operation 3559
license: Apache-2.0

GScluster
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0128
application sub category: topic 3517
application sub category: topic 3518
citation: S12864-019-5738-6
citation: pmcid:PMC6507172
citation: pubmed:31072324
description: Package for network-weighted gene-set clustering and network visualization.
feature list: operation 2436
feature list: operation 2492
feature list: operation 3432
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: GScluster manual v1.1.6.pdf
primary contact: https://orcid.org/0000-0003-0239-2899
primary contact: Seon-Young Kim

GTA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0622
application sub category: topic_0623
application sub category: topic 3293
citation: EVZ206
citation: pmcid:PMC6821227
citation: pubmed:31560374
description: GTA_Hunter is a 'support-vector machine' (SVM) classifier that distinguishes gene transfer agent (GTA) genes from their viral homologs | The classifier was developed to detect GTA genes that are homologous to 11 of the genes that encode the GTA in Rhodobacter capsulatus (RcGTA) (see Kogay et al, 2019). However, the classifier can be trained to detect other RcGTA genes, other GTAs, or even other virus-like elements, as long as there is training data available and the two classes have distinct amino acid composition
feature list: operation 3431
feature list: operation 3501
license: MIT

GTACG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0623
application sub category: topic_0625
application sub category: topic_0780
citation: FGENE.2019.00725
citation: pmcid:PMC6718126
citation: pubmed:31507629
description: A User-Friendly Framework for Bacterial Comparative Genomics | Backend application for the GTACG project (Gene Tags Assessment by Comparative Genomics) | Frontend application for the GTACG project (Gene Tags Assessment by Comparative Genomics) | This project is the frontend part of the GTACG framework (Gene Tags Assessment by Comparative Genomics): a framework for comparative analysis of bacterial genomes | A proper execution of the GTACG pipeline requires at least genomic files (in fasta format) and coding sequences (CDS, faa, gbf, gb, gff) files. Additionally, you can define phenotypes groups. The following command lines can be used to download files with examples of these formats:
feature list: operation 3192
license: GPL-3.0

GTCreator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3382
citation: s11548-018-1864-x
citation: pubmed:30255462
description: Annotation tool for providing image and text annotations to image-based datasets.
feature list: operation 3553
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: CVC-Colon

GTDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0194
application sub category: topic_0637
application sub category: topic 3174
citation: s41564-021-00918-8
citation: s41587-020-0501-8
citation: gkab776
citation: https://doi.org/10.1101/771964
citation: pmcid:PMC8728215
citation: pubmed:32341564
citation: pubmed:34155373
citation: pubmed:34520557
description: Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy | Toolkit for establishing, updating, and validating GTDB species clusters
feature list: operation_0544
feature list: operation 3432
feature list: operation 3460
license: GPL-3.0

GTDB-Tk
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0078
application sub category: topic_0637
application sub category: topic 3174
application sub category: topic 3293
application sub category: topic 3489
citation: btz848
citation: pmcid:PMC7703759
citation: pubmed:31730192
description: a toolkit to classify genomes with the Genome Taxonomy Database. GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).
feature list: operation_0224
feature list: operation_0310
feature list: operation 3182
feature list: operation 3460
license: GPL-3.0

GTM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0194
citation: https://doi.org/10.1101/835959
description: Unblended Disjoint Tree Merging using GTM improves species tree estimation. Abstract Phylogeny estimation is an important part of much biological research, but large-scale tree estimation is infeasible using standard methods due to computational issues. Recently, an approach to large-scale phylogeny has been proposed that divides a set of species into disjoint subsets, computes trees on the subsets, and then merges the trees together using a computed matrix of pairwise distances between the species. The novel component of these approaches is the last step: Disjoint Tree Merger (DTM) methods. We present GTM (Guide Tree Merger), a polynomial time DTM method that adds edges to connect the subset trees, so as to provably minimize the topological distance to a computed guide tree. Thus, GTM performs unblended mergers, unlike the previous DTM methods
feature list: operation_0325
feature list: operation_0546
feature list: operation 3478

GUESSmyLT
type: SoftwareApplication
input: Gene map
  type: FormalParameter
  additional type: data 1285
  encoding format: format 1996
  encoding format: format 3285
input: Gene report
  type: FormalParameter
  additional type: data_0916
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 3170
citation: joss.01344
description: Software to guess the RNA-Seq library type of paired and single end read files using mapping and gene annotation.
feature list: operation_0362
is accessible for free: true
license: GPL-3.0
software help: GUESSmyLT
software version: v1.0

GUV-AP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0154
application sub category: topic_0820
application sub category: topic 3382
citation: bty962
citation: pubmed:30475993
description: Multifunctional FIJI-based tool for quantitative image analysis of Giant Unilamellar Vesicles.
feature list: operation 3454
feature list: operation 3799
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: GUV-AP manual.pdf
software help: README.md
software version: 2.0
primary contact: Winfried Römer
primary contact: Yves Mély

GUcal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3489
application sub category: topic 3520
citation: CWZ102
citation: pubmed:31829415
description: Expanding the capillary electrophoresis based glucose unit database of the GUcal app. GUcal 1.1c - Internal / bracketing standard approach with GlycoStore database
feature list: operation 3435

GW6 - Grand-average ERP algorithm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3304
application sub category: topic 3315
description: GW6 algorithm for multichannel EEG data
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: marco.bilucaglia

GWAS-Flow
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3517
citation: https://doi.org/10.1101/783100
description: A GPU accelerated framework for efficient permutation based genome-wide association studies | GPU accelerated GWAS framework based on TensorFlow | GWAS-Flow was written and published in the hope that you might find it useful. If you do and use it for your research please cite the paper published alongside the software, which is currently publicly accessible on the BiorXiv preprint server. https://www.biorxiv.org/content/10.1101/783100v1 doi: 10.1101/783100
feature list: operation 3196
feature list: operation 3557
feature list: operation 3891
license: MIT

GWAS Central
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3517
application sub category: topic 3574
citation: gkz895
citation: pmcid:PMC7145571
citation: pubmed:31612961
description: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies. A database for human genetic variants identified by genome-wide association studies. Enter a study id, dbSNP id, MeSH/HPO phenotype term, keywords, author names, HGNC gene symbols, chromosomal regions or PUBMED identifier. The NHGRI-EBI GWAS Catalog: a curated collection of all published genome-wide association studies, produced by a collaboration between EMBL-EBI and NHGRI. GWAS CENTRAL - INDIA : A Genotype - Phenotype Association Database. GWAS Central - India (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. GWAS Central provides a complete Study metadata file for use in data citation research, tracking researcher contributions, data discovery projects, etc
feature list: operation 2421
feature list: operation 3196
feature list: operation 3436
feature list: operation 3559
feature list: operation 3791
software help: gwas-central-study-meta-data

GWASinlps
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3517
citation: bty472
citation: pmcid:PMC6298063
citation: pubmed:29931045
description: Non-local prior based iterative SNP selection tool for genome-wide association studies.
feature list: operation_0484
feature list: operation 3659
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: GWASinlps.pdf
software version: 1.2
primary contact: Nilotpal Sanyal

GWASinspector
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3517
application sub category: topic 3572
description: When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.3.4

GWPC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0593
application sub category: topic 3384
application sub category: topic 3444
citation: https://doi.org/10.1101/750117
description: Increased contrast of the grey-white matter boundary in the motor, visual and auditory areas in Autism Spectrum Disorders | Grey-to-White matter Percent Contrast in Autism Spectrum Disorders | This repository contains the code used for the analyses described in our manuscript "Increased contrast of the grey-white matter boundary in the motor, visual and auditory areas in Autism Spectrum Disorders" (Preprint: https://doi.org10.1101/750117) | We used this code to analyse the grey-white contrast in Autism Spectrum Disorder using magnetic resonance imaging from ABIDE 1&2 datasets (http://fcon_1000.projects.nitrc.org/indi/abide/)
feature list: operation 3435
feature list: operation 3557
feature list: operation 3659

GalaxEast
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic 3391
description: GalaxEast aims at providing a large range of bioinformatics tools for the analysis of various types of Omics data. It supports reproducible computational research by providing an environment for performing and recording bioinformatics analyses.

GalaxyCat
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
description: An online catalog that lists all the tools available on various Galaxy instances and thus allows through a simple web interface to quickly find on which instances a tool is usable.

Galaxy Pasteur
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic_0080
description: A wide variety of tools from the Galaxy instance of Institut Pasteur, France.

Galaxy Tools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
description: Tools provided by the Galaxy workbench.
is accessible for free: true
license: AFL-2.0
operating system: Linux
operating system: Mac
primary contact: Galaxy Project

Galaxy scater
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
citation: https://doi.org/10.1101/724047
description: We have developed a range of practical scripts, together with their corresponding Galaxy wrappers, that make scRNA-seq training and quality-control accessible to researchers previously daunted by the prospect of scRNA-seq analysis. We implement a ‘visualise-filter-visualise’ paradigm through simple command-line tools that use the Loom format to exchange data between the tools. The point-and-click nature of Galaxy makes it easy to assess, visualise, and filter scRNA-seq data from short-read sequencing data.
feature list: operation_0571
feature list: operation 3563
is accessible for free: true
license: AFL-3.0
software help: scater
primary contact: https://orcid.org/0000-0002-5003-1425

Gall-ID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
application sub category: topic_0084
application sub category: topic_0637
application sub category: topic_0780
application sub category: topic 3673
application sub category: topic 3810
citation: peerj.2222
citation: pmcid:PMC4958008
citation: pubmed:27547538
description: Tools for genotyping gall-causing phytopathogenic bacteria and identifying strains isolated from Agrobacterium or Rhodococcus-induced galls using MLSA and other methods.
feature list: operation 2421
feature list: operation 3192
feature list: operation 3196
is accessible for free: true

GapMind
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic_0798
citation: https://doi.org/10.1101/741918
description: Automated annotation of amino acid biosynthesis | Abstract GapMind is a web-based tool for annotating amino acid biosynthesis in bacteria and archaea ( http: papers.genomics.lbl gov gaps ). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 seconds. To avoid error-prone “transitive” annotations, GapMind relies primarily on a database of experimentally-characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for “best hit” approaches. To improve GapMind’s coverage, we examined genetic data from 35 bacteria that grow in minimal media and we filled many gaps in amino acid biosynthesis pathways.
feature list: operation_0417
feature list: operation 3715

Gapsplit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic 3398
application sub category: topic 3407
citation: https://doi.org/10.1101/652917
description: Efficient random sampling for constraint-based (COBRA) models.
feature list: operation 3660
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Paul A. Jensen

Garnett
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 3170
citation: S41592-019-0535-3
citation: pmcid:PMC6791524
citation: pubmed:31501545
description: Supervised classification enables rapid annotation of cell atlases | Garnett - Automated cell type identification
feature list: operation 2495
feature list: operation 3233
feature list: operation 3501

GazeVisual-Lib
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3382
application sub category: topic 3474
application sub category: topic 3572
citation: VISION3040055
citation: pubmed:31735856
description: Development of Open-source Software and Gaze Data Repositories for Performance Evaluation of Eye Tracking Systems. Repository for GazeVisual performance evaluation software tools. The GazeVisual-Lib is a repository of software tools for practical evaluation of eye trackers and gaze data quality. All codes in this repository are released under GNU General Public License v3.0
feature list: operation_0337
feature list: operation 1812
feature list: operation 3799
feature list: operation 3891
license: GPL-3.0

GeDex
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
application sub category: topic 3068
application sub category: topic 3322
application sub category: topic 3474
application sub category: topic 3517
citation: https://doi.org/10.1101/839704
description: A consensus Gene-disease Event Extraction System based on frequency patterns and supervised learning. Abstract Motivation The genetic mechanisms involved in human diseases are fundamental in biomedical research. Several databases with curated associations between genes and diseases have emerged in the last decades. Although, due to the demanding and time consuming nature of manual curation of literature, they still lack large amounts of information. Current automatic approaches extract associations by considering each abstract or sentence independently. This approach could potentially lead to contradictions between individual cases. Therefore, there is a current need for automatic strategies that can provide a literature consensus of gene-disease associations, and are not prone to making contradictory predictions
feature list: operation 3196
feature list: operation 3280

GeNeCK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3308
citation: s12859-018-2560-0
citation: pmcid:PMC6323745
citation: pubmed:30616521
description: GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information.
feature list: operation_0277
feature list: operation 1781
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: analysis.php
software version: 1.0
primary contact: Minzhe Zhang

GePhEx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2885
application sub category: topic 3298
application sub category: topic 3517
citation: btz622
citation: pubmed:31393550
description: Genome-Phenome Explorer (GePhEx): A tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence.
feature list: operation_0484
feature list: operation 2422
feature list: operation 3625
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: doc

GemSIM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3168
description: GemSIM is a software package for generating realistic simulated next-generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using appropriate empirical error models.
is accessible for free: true
license: GPL-3.0
software help: files

GenAPI
type: SoftwareApplication
input: Nucleic acid sequence record
  type: FormalParameter
  additional type: data 2887
  encoding format: format 1939
output: Phylogenetic tree
  type: FormalParameter
  additional type: data_0872
  encoding format: format 1910
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 3508
output: Matrix
  type: FormalParameter
  additional type: data 2082
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0091
application sub category: topic_0622
citation: https://doi.org/10.1101/658476
description: Program for gene presence-absence analysis for series of closely related bacterial genomes from annotated GFF files.
feature list: operation 2478
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: GenAPI
primary contact: Migle Gabrielaite

GenBank Flat File Reader
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0622
application sub category: topic 3053
application sub category: topic 3344
description: Read GenBank-formatted flat file into structure
feature list: operation 1812
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: Turner Conrad

GenBank taxonomy tools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0637
description: Utilities for manipulations and visualization tasks on GenBank taxonomic information.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md

GenESysV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0625
application sub category: topic 3673
application sub category: topic 3676
citation: s12859-019-2636-5
citation: pmcid:PMC6357466
citation: pubmed:30704396
description: Genome exploration open source tool for variants generated from high-throughput sequencing projects.
feature list: operation 2422
feature list: operation 3196
feature list: operation 3227
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
primary contact: Center for Computational Research

GenFam
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0203
application sub category: topic_0623
application sub category: topic_0780
application sub category: topic 3170
citation: PLD3.191
citation: pmcid:PMC6892992
citation: pubmed:31844835
description: A web application and database for gene family-based classification and functional enrichment analysis. Genome-scale studies using high-throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popular approach is to determine statistically overrepresented genes in a user-defined list through enrichment analysis tools, which rely on functional annotations of genes based on Gene Ontology (GO) terms. Here, we propose a new computational approach, GenFam, which allows annotation, classification, and enrichment of genes based on their gene family, thus simplifying identification of candidate gene families and associated genes that may be relevant to the query.
feature list: operation_0224
feature list: operation 2436
feature list: operation 3672

GenGraph
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0622
application sub category: topic 3673
citation: S12859-019-3115-8
citation: pmcid:PMC6894214
citation: pubmed:31653197
description: a python module for the simple generation and manipulation of genome graphs. A repository for the GenGraph toolkit for the creation and manipulation of graph genomes
feature list: operation_0337
feature list: operation_0492
feature list: operation_0524
feature list: operation 3182
license: GPL-3.0

GenIE-Sys
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3489
application sub category: topic 3571
citation: https://doi.org/10.1101/808881
description: Genome Integrative Explorer System. Genome Integrative Explorer System (GenIE-Sys). Website : Documentation : Demo : Users. Welcome to GenIE-Sys’s documentation! — GenIE-Sys 0.1 documentation. The Genome Integrative Explorer System(GenIE-Sys) based on a flat files Content Management System which is a dedicative in-house system to facilitate external groups in setting up their own web resource for searching, visualizing, editing, sharing and reproducing their genomic and transcriptomic data while using project raw data(gff3,fasta,fatsq) as an input. This is the Development and the latest version of GenIE-Sys. Our main goal is to add admin interface where users can easily create database plus integrate different types of data, create new pages and menus, configure tools and changing website layout by using Themes. Free document hosting provided by Read the Docs
feature list: operation_0337
feature list: operation 2421
feature list: operation 3096
license: BSD-3-Clause
software help: geniesys.readthedocs.io

GenIO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic 3063
application sub category: topic 3325
application sub category: topic 3676
citation: s12859-018-2027-3
citation: pmcid:PMC5787240
citation: pubmed:29374474
description: Genomic Input Output (GenIO) identifies the most probable variants causing a rare disease, using the genomic and clinical information provided by a medical practitioner.
feature list: operation 3196
feature list: operation 3229
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.htm
software version: 1.0

GenTree
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0102
application sub category: topic_0121
application sub category: topic 3512
citation: gr.238733.118
citation: pmcid:PMC6442393
citation: pubmed:30862647
description: Integrated resource for analyzing the evolution and function of primate-specific coding genes.
feature list: operation_0487
feature list: operation 3501
feature list: operation 3766
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: ZhangLab

Gene2vec
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0659
citation: s12864-018-5370-x
citation: pmcid:PMC6360648
citation: pubmed:30712510
description: Machine learning method that utilizes transcriptome-wide gene co-expression to generate a distributed representation of genes.
feature list: operation_0315
feature list: operation 3439
feature list: operation 3766
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
primary contact: Jingcheng Du

Gene4Denovo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3170
application sub category: topic 3673
application sub category: topic 3676
citation: gkz923
citation: pmcid:PMC7145562
citation: pubmed:31642496
description: an integrated database and analytic platform for de novo mutations in humans. De novo mutations (DNMs) significantly contribute to sporadic diseases, particularly in neuropsychiatric disorders. Whole-exome sequencing (WES) and whole-genome sequencing (WGS) provide effective methods for detecting DNMs and prioritizing candidate genes. However, it remains a challenge for scientists, clinicians, and biologists to conveniently access and analyse data regarding DNMs and candidate genes from scattered publications. To fill the unmet need, we integrated 580 799 DNMs, including 30 060 coding DNMs detected by WES WGS from 23 951 individuals across 24 phenotypes and prioritized a list of candidate genes with different degrees of statistical evidence, including 346 genes with false discovery rates <0.05. We then developed a database called Gene4Denovo (http: www.genemed.tech gene4denovo ), which allowed these genetic data to be conveniently catalogued, searched, browsed, and analysed
feature list: operation 2421
feature list: operation 3196
feature list: operation 3226
feature list: operation 3461

GeneBridge
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0153
application sub category: topic_0203
application sub category: topic_0621
application sub category: topic_0625
application sub category: topic 2229
citation: GR.251983.119
citation: pmcid:PMC6886503
citation: pubmed:31754022
description: Identifying gene function and module connections by the integration of multispecies expression compendia. Integrative systems analysis identifying the associations between genes and biological process or modules. For analyzed results for a given gene or module/gene set, please visit https://systems-genetics.org/genebridge. Systems analysis toolkit containing Gene-Module Association Determination (G-MAD) and Module-Module Association Determination (M-MAD) to identify the associations between genes and biological process or modules, as well as associations between modules.
feature list: operation 2436
feature list: operation 3557
feature list: operation 3672
license: GPL-3.0

GeneMarkS-T
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic_0621
description: Sets of assembled eukaryotic transcripts can be analyzed by the modified GeneMarkS algorithm (the set should be large enough to permit self-training). A single transcript can be analyzed by a special version of GeneMark.hmm with Heuristic models. A new advanced algorithm GeneMarkS-T was developed recently (manuscript sent to publisher).
feature list: operation_0310

GenePattern notebook
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic 2885
application sub category: topic 3295
application sub category: topic 3518
citation: F1000RESEARCH.16338.1
citation: pmcid:PMC6498745
citation: pubmed:31105932
description: Analysis of copy number variation using Illumina Infinium DNA methylation arrays.
feature list: operation 3219
feature list: operation 3436
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: faq
software help: tutorials
primary contact: https://orcid.org/0000-0001-9926-5209
primary contact: https://orcid.org/0000-0002-8718-8848

GenePy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Script
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3676
citation: s12859-019-2877-3
citation: pmcid:PMC6524327
citation: pubmed:31096927
description: Score for estimating gene pathogenicity in individuals using next-generation sequencing data.
feature list: operation 3196
feature list: operation 3227
feature list: operation 3435
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: README.md

GeneRax
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0102
application sub category: topic_0194
citation: https://doi.org/10.1101/779066
description: A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss | GeneRax is a parallel tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss
feature list: operation_0544
feature list: operation_0547
feature list: operation_0552
license: AGPL-3.0

GeneSurrounder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0634
citation: S12859-019-2829-Y
citation: pmcid:PMC6503437
citation: pubmed:31060502
description: Network-based identification of disease genes in expression data.
feature list: operation_0277
feature list: operation 2436
feature list: operation 3463
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Rosemary Braun
primary contact: Sahil Shah

GeneSwitches
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3295
citation: https://doi.org/10.1101/832626
description: Ordering gene-expression and functional events in single-cell experiments. Data-driven Network Biology Group. The goal of GeneSwitches is to discover the order of gene-expression and functional events during cell state transitions at a single-cell resolution. It works on any single-cell trajectory or pseudo-time ordering of cells to discover the genes that act as on/off switches between cell states and importantly the ordering at which these switches take place.
feature list: operation 2495
feature list: operation 3659
feature list: operation 3890
software help: GeneSwitches SI.pdf

GeneVetter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0625
application sub category: topic 3325
citation: btv432
citation: pmcid:PMC4643620
citation: pubmed:26209433
description: Investigation of the background prevalence (rare, protein altering variants that could be classified as pathogenic) of exonic variation.
feature list: operation 3196
feature list: operation 3227
feature list: operation 3461
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: genevetter.kidneyomics.org
primary contact: Matthew Gordon Sampson

GeneWalk
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 3170
citation: s13059-021-02264-8
citation: pmcid:PMC7852222
citation: pubmed:33526072
description: GeneWalk identifies relevant gene functions for a biological context using network representation learning | GeneWalk determines for individual genes the functions that are relevant in a particular biological context and experimental condition. GeneWalk quantifies the similarity between vector representations of a gene and annotated GO terms through representation learning with random walks on a condition-specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks
feature list: operation_0277
feature list: operation 1781
feature list: operation 2436
license: BSD-2-Clause

GeneYenta
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic_0625
application sub category: topic 3325
application sub category: topic 3676
author: David Arenillas
author: Zach Maurer
citation: humu.22772
citation: pubmed:25703386
description: Tool for clinicians to make connections to share genetic data by being matched using phenotype data. It aims to create a portal for clinicians to enter phenotypic case data for individuals who have had exome sequencing without a genetic diagnosis.
feature list: operation 3227
feature list: operation 3229
feature list: operation 3431
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: GeneYenta

Gene Sculpt Suite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
additional type: Web application
application sub category: topic 3474
application sub category: topic 3512
application sub category: topic 3912
citation: GKZ405
citation: pmcid:PMC6602503
citation: pubmed:31127311
description: Set of tools for assisting in highly precise genome editing and engineering.
feature list: operation_0420
feature list: operation 3096
feature list: operation 3198
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0001-5930-4111
primary contact: Jeffrey J. Essner
primary contact: Stephen C. Ekker

GeneRecommender
type: SoftwareApplication
input: Gene identifier
  type: FormalParameter
  additional type: data 1025
  encoding format: format 2330
  encoding format: format 2350
output: Database search results
  type: FormalParameter
  additional type: data 2080
  encoding format: format 2848
  encoding format: format 3617
  encoding format: format 3620
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
application sub category: topic_0602
application sub category: topic 3070
application sub category: topic 3344
application sub category: topic 3474
application sub category: topic 3948
description: Platform based on Artificial Intelligence Neural Network. Suggest the most probable gene (protein) based on deep learning on million of scientific papers. It also link the input+output to many free research tools to understand what the neural network suggested and why.
feature list: operation 2436
feature list: operation 3279
feature list: operation 3625
feature list: operation 3767
feature list: operation 3929
is accessible for free: true
license: Freeware
operating system: Linux
operating system: Mac
operating system: Windows
software help: arXiv.2208.01918
software version: 2 stable

Geneshot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3170
citation: GKZ393
citation: pmcid:PMC6602493
citation: pubmed:31114885
description: search engine for ranking genes from arbitrary text queries | Submit biomedical terms to receive ranked lists of relevant genes | Submit any search terms to Geneshot to receive prioritized genes that are most relevant to the search terms. Geneshot finds publications that mention both the search terms and genes. It then prioritizes these genes using various methods: 1) list of genes from publications; 2) predicted genes using gene-gene similarity matrices derived from a variety of resources ( ARCHS4 : Enrichr : Tagger : AutoRIF : GeneRIF ) | Examples: Wound healing : Hair loss : Trichostatin A : Glioblastoma : Diabetes
feature list: operation 2436
feature list: operation 2454
feature list: operation 3463
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: https://orcid.org/0000-0002-6904-1017
primary contact: Alexander Lachmann

Genesis-indel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic 3168
citation: S41598-019-47405-Z
citation: pmcid:PMC6668410
citation: pubmed:31366961
description: > LOW CONFIDENCE! | Uncovering missed indels by leveraging unmapped reads | Genesis-indel is a computational pipeline to explore the unmapped reads to identify novel mutations that are initially missed in the original alignment. The genes containing such mutations can be investigated to gain important biological insights
feature list: operation_0452
feature list: operation 3198
feature list: operation 3227
license: MIT

GenoGeographer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2885
application sub category: topic 3068
application sub category: topic 3168
application sub category: topic 3305
citation: J.FSIGEN.2019.102154
citation: pubmed:31670023
description: Ancestry prediction efficiency of the software GenoGeographer using a z-score method and the ancestry informative markers in the Precision ID Ancestry Panel. A tool for genogeographic inference
feature list: operation_0484
feature list: operation 3196
feature list: operation 3435

GenoSurf
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0089
application sub category: topic_0091
application sub category: topic_0622
application sub category: topic 2815
application sub category: topic 3489
citation: 978-3-030-85918-3 8
citation: baz132
citation: pmcid:PMC6902006
citation: pubmed:31820804
contributor: https://orcid.org/0000-0001-8016-5750
contributor: https://orcid.org/0000-0003-0671-2415
description: GenoSurf is a metadata driven semantic search system for integrated genomic datasets. Many valuable resources developed by worldwide research institutions and consortia describe genomic datasets that are open, but their metadata search interfaces are heterogeneous, not interoperable, and with limited capabilities. GenoSurf provides access to a consolidated collection of metadata attributes found in the most relevant genomic datasets; values of attributes are semantically enriched by making use of the most suited available ontologies. Users provide as input the search terms, set the desired level of ontological enrichment, and obtain as output the identity of matching data files at the various sources. We integrated about 40 million metadata of several major valuable data sources, including four providers of clinical and experimental data (TCGA, ENCODE, 1000 Genomes, and Roadmap Epigenomics) and two sources of annotation data (GENCODE and RefSeq).
feature list: operation_0224
feature list: operation 2421
feature list: operation 2422
feature list: operation 3436
software help: api
software help: wiki
primary contact: https://orcid.org/0000-0003-4528-6586

Genoma
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0622
description: Database of genomic data related to marine species of biological interest. It allows analyses of reference genome annotations, organising the resources in an integrated way
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: section1

Genome3D
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0621
application sub category: topic_0769
citation: GKZ967
citation: pubmed:31733063
description: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. Genome3D Annotating Genomes with Structures. Search Genome3D find structural annotations for your proteins. Tool to interact with the Genome3D API. Genome3D provides consensus structural annotations and 3D models for sequences from model organisms, including human. These data are generated by several UK based resources in the Genome3D consortium: SCOP, CATH, SUPERFAMILY, Gene3D, FUGUE, THREADER, PHYRE. The tool genome3d-api aims to make communicating with the Genome3D API as convenient as possible. However, since the API has been defined using OpenAPI standards, you should be able to point any OpenAPI compatible client to the following specification:
feature list: operation_0303
feature list: operation 2421
feature list: operation 2422
feature list: operation 3778
license: GPL-3.0
software help: api

GenomeFlow
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic_0621
application sub category: topic_0654
citation: bty802
citation: pmcid:PMC6477968
citation: pubmed:30215673
description: Graphical tool for modeling and analyzing 3D genome structure.
feature list: operation 2429
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: wiki
primary contact: Jianlin Cheng

GenomeHubs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic_0769
application sub category: topic_0780
application sub category: topic 3489
citation: PEERJ.PREPRINTS.2401V2
description: Simple containerised setup of a custom Ensembl database and web server for any species. Forked from molluscdb/molluscdb-plugin. Example configurations to set up custom Ensembl sites using GenomeHubs. GenomeHubs example configuration and demo script. Generic Ensembl plugin for genomehubs sites. GenomeHubs is designed to make it easy to set up and host a core set of bioinformatics tools to help research communities share and access genomic datasets for non-model organisms. Sets up a GenomeHubs site hosting a mirror of the core database for the Glanville fritillary, Melitaea cinxia and imports the genome of the winter moth, Operophtera brumata, into a GenomeHubs site from FASTA and GFF.
feature list: operation_0310
feature list: operation_0335
feature list: operation 3208
license: MIT
software help: demo

GenomeQC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic_0622
application sub category: topic 3168
application sub category: topic 3500
application sub category: topic 3810
citation: https://doi.org/10.1101/795237
description: A quality assessment tool for genome assemblies and gene structure annotations. GenomeQC generates descriptive summaries with intuitive graphics for genome assembly and structural annotations. It also benchmarks user supplied assemblies and annotations against the publicly available reference genomes of their choice. It is optimized for small and medium sized genomes (<2.5 Gb) and has pre-computed results for several maize genomes.
feature list: operation_0362
feature list: operation_0525
feature list: operation 3216
license: GPL-3.0

Genome Constellation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0194
application sub category: topic_0196
application sub category: topic_0637
application sub category: topic 3174
application sub category: topic 3293
citation: https://doi.org/10.1101/812917
description: A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome. About Press Copyright Contact us Creators Advertise Developers Terms Privacy Policy & Safety Test new features.
feature list: operation_0337
feature list: operation_0525
feature list: operation 3432

Genomic GPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0622
application sub category: topic 3263
citation: S13059-019-1792-2
citation: pmcid:PMC6712716
citation: pubmed:31455387
description: Using genetic distance from individuals to public data for genomic analysis without disclosing personal genomes | # 2019 Bioinformatics Methods / GenomicGPS | GenomicGPS is a software package for applying multilateration to genomic data
feature list: operation_0487
feature list: operation 3196
feature list: operation 3891
license: MIT

GenomicsDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3337
application sub category: topic 3396
application sub category: topic 3423
application sub category: topic 3577
application sub category: topic 3676
citation: https://doi.org/10.1101/841940
description: Advancing clinical cohort selection with genomics analysis on a distributed platform. Highly performant data storage in C++ for importing, querying and transforming variant data with Java/Spark. Used in gatk4. Sparse Array Storage for Genomics. GenomicsDB, originally from Intel Health and Lifesciences, is built on top of a fork of htslib and a tile-based array storage system for importing, querying and transforming variant data. Open source project providing a collaboration to optimizing sparse array storage for genomics. Using high-level APIs provided in C++, Java*, and Spark*, users can both write and read variant records to and from GenomicsDB shared-nothing instances in parallel using multiple processes in a Single Process Multiple Data (SPMD) manner.
feature list: operation_0224
feature list: operation 3227
feature list: operation 3436

Genomicus-plants
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic_0623
application sub category: topic_0780
application sub category: topic_0797
application sub category: topic 3299
application sub category: topic 3943
citation: btq079
citation: gks1156
citation: gku1112
citation: gkx1003
citation: pcu177
description: Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
feature list: operation_0224
feature list: operation_0490
feature list: operation_0567
feature list: operation 3208
is accessible for free: true
primary contact: http://orcid.org/0000-0001-7032-5650
primary contact: 0000-0002-8209-173X

Genomicus-fungi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0194
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic_0623
application sub category: topic_0797
application sub category: topic 3299
application sub category: topic 3943
citation: btq079
citation: gks1156
citation: gku1112
citation: gkx1003
description: Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
feature list: operation_0224
feature list: operation_0490
feature list: operation_0567
feature list: operation 3208
is accessible for free: true
primary contact: http://orcid.org/0000-0001-7032-5650
primary contact: 0000-0002-8209-173X

Genomicus-metazoa
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0194
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic_0623
application sub category: topic_0797
application sub category: topic 3299
application sub category: topic 3943
citation: btq079
citation: gks1156
citation: gku1112
citation: gkx1003
citation: pmcid:PMC2853686
citation: pmcid:PMC3531091
citation: pmcid:PMC4383929
citation: pmcid:PMC5753199
citation: pubmed:20185404
citation: pubmed:23193262
citation: pubmed:25378326
citation: pubmed:29087490
description: Genomicus-metazoa is a genome browser that enables users to navigate in metazoa genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
feature list: operation_0224
feature list: operation_0490
feature list: operation_0567
feature list: operation 3208
is accessible for free: true
primary contact: http://orcid.org/0000-0001-7032-5650
primary contact: 0000-0002-8209-173X

Genomicus-protists
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0194
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic_0623
application sub category: topic_0797
application sub category: topic 3299
application sub category: topic 3943
citation: btq079
citation: gks1156
citation: gku1112
citation: gkx1003
description: Genomicus-protists is a genome browser that enables users to navigate in protists genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
feature list: operation_0224
feature list: operation_0490
feature list: operation_0567
feature list: operation 3208
is accessible for free: true
primary contact: http://orcid.org/0000-0001-7032-5650
primary contact: 0000-0002-8209-173X

Genomicus-tunicates
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0194
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic_0623
application sub category: topic_0797
application sub category: topic 3299
application sub category: topic 3943
citation: gkx1108
citation: gkz955
citation: pmcid:PMC5753386
citation: pmcid:PMC7145539
citation: pubmed:29149270
citation: pubmed:31680137
description: Genomicus-tunicates is a genome browser that enables users to navigate in tunicates genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. It uses ANISEED (https://www.aniseed.cnrs.fr) database.
feature list: operation_0224
feature list: operation_0490
feature list: operation_0567
feature list: operation 3208
is accessible for free: true
primary contact: http://orcid.org/0000-0001-7032-5650
primary contact: 0000-0002-8209-173X

Genotom
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3308
description: A multigenome platform with information on genomes and gene annotations from different tomato cultivars. This platform includes genomes from Heinz 1706, Lucariello and Corbarino (tomato landaraces) with related genome browsers and transcriptomic data. It gives free access to the recently sequenced Italian tomato varieties and offers tools for their comparative analysis. (Tranchida-Lombardo et al., ‎2017; https://doi.org/10.1093/dnares/dsx045)
feature list: operation 3208
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1

Genus biomolecules
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0078
application sub category: topic_0097
application sub category: topic_0099
application sub category: topic_0196
application sub category: topic 3489
citation: GKZ845
citation: pubmed:31584078
description: A database of genus characteristics of proteins and RNA. A database of genus characteristics. The Genus database collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given chain and its subchains. For each biomolecule this information is shown in the form of a genus trace plot, as well as a genus matrix diagram. We assemble such information for all protein and RNA structures deposited in the PDB. This database presents also various statistics and extensive information about biological function of analyzed biomolecules. Moreover, users can analyze their own structures
feature list: operation_0337
feature list: operation 2421
feature list: operation 3431

GeoNode-Tools4MSP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0610
application sub category: topic_0769
application sub category: topic 3489
application sub category: topic 3855
citation: PEERJ.PREPRINTS.2245V2
description: Open source tools to support Integrated Coastal Management and Maritime Spatial Planning. Geospatial tools to support Maritime Spatial Planning. GeoNode is a web-based application and platform for developing geospatial information systems (GIS) and for deploying spatial data infrastructures (SDI). Tools4MSP is a python-based Free and Open Source Software (FOSS) for geospatial analysis in support of Maritime Spatial Planning (MSP) and marine environmental management. Tools4MSP implements models for Cumulative Effects Assessment (CEA), Maritime Use Conflict (MUC) Analysis and Marine Ecosystem Services Threat (MES-Threat) analysis. The package can be used as stand-alone library or as integrated GeoNode Plugin providing additional functionalities to geospatial CMS and enhancing usability through a graphical user interface (GUI). Gallery Quick Start Try the Demo Blog. The webtools (GeoNode integration) analysis workflow follows a four step approach:
feature list: operation 3436
feature list: operation 3760
license: GPL-3.0

Gephebase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic_0780
citation: gkz796
citation: pmcid:PMC6943045
citation: pubmed:31544935
description: database of genotype-phenotype relationships for natural and domesticated variation in Eukaryotes | Gephebase compiles genotype-phenotype relationships, i.e. associations between a mutation and a phenotypic variation. Gephebase consolidates data from the scientific literature about the genes and the mutations responsible for phenotypic variation in Eukaryotes (mostly animals, yeasts and plants). We plan to include non Eukaryote species in the future. For now, genes responsible for human disease and for aberrant mutant phenotypes in laboratory model organisms are excluded and can be found in other databases ( OMIM , OMIA , FlyBase , etc.). QTL mapping studies that did not identify single genes are not included in Gephebase | If you use Gephebase for your publication, please cite: Martin, A., & Orgogozo, V. (2013). The loci of repeated evolution: a catalog of genetic hotspots of phenotypic variation. Evolution, 67(5), 1235- 1250
feature list: operation_0282
feature list: operation 3501

GerOSS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3325
application sub category: topic 3411
citation: ME14-01-0141
citation: pubmed:26065375
description: German Obstetric Surveillance System (GerOSS) - project to improve the treatment of obstetric rare diseases and complications using a web based documentation and information platform.
feature list: operation 3283
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Nicholas Lack
primary contact: Silvia Berlage

DUNE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3384
citation: https://doi.org/10.1101/2025.02.24.25322787
description: A versatile neuroimaging encoder for extracting deep features from multisequence brain MRIs
feature list: operation 3937
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

Gigwa
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3071
citation: GIZ051
citation: s13742-016-0131-8
citation: pmcid:PMC4897896
citation: pmcid:PMC6511067
citation: pubmed:27267926
citation: pubmed:31077313
description: The Gigwa application, which stands for “Genotype Investigator for Genome-Wide Analyses”, provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype patterns. It is a fairly lightweight, web-based, platform-independent solution that may be deployed on a workstation or as a data portal. It allows to feed a MongoDB database with VCF, PLINK or HapMap files containing up to tens of billions of genotypes, and provides a user-friendly interface to filter data in real time. Gigwa provides the means to export filtered data into several popular formats and features connectivity not only with online genomic tools, but also with standalone software such as FlapJack or IGV. Additionnally, Gigwa-hosted datasets are interoperable via two standard REST APIs: GA4GH and BrAPI.
feature list: operation_0337
feature list: operation 2409
feature list: operation 3196
feature list: operation 3695
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: gigwa docs.html
software version: 2.3
primary contact: https://orcid.org/0000-0001-7429-2091

GiniClust3
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/788554
description: A fast and memory-efficient tool for rare cell type identification. Rare cell identification tool for single cell datasets. GiniClust is a clustering method specifically designed for rare cell type detection.
feature list: operation 3432
feature list: operation 3435
feature list: operation 3659

GkmExplain
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3168
application sub category: topic 3474
citation: BTZ322
citation: pmcid:PMC6612808
citation: pubmed:31510661
description: Fast and accurate interpretation of nonlinear gapped k-mer SVMs | Accompanying repository for GkmExplain paper | GkmExplain: Fast and Accurate Interpretation of Nonlinear Gapped k-mer Support Vector Machines | This repository accompanies Gkmexplain: Fast and Accurate Interpretation of Nonlinear Gapped k-mer SVMs by Shrikumar*†, Prakash* and Kundaje† (*co-first authors †co-corresponding authors).
feature list: operation_0238
feature list: operation 3472
feature list: operation 3501

Glutton
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0154
application sub category: topic_0593
application sub category: topic 3444
citation: bty755
citation: pubmed:30184055
description: Tool for generating structural ensembles of partly disordered proteins from chemical shifts.
feature list: operation_0249
feature list: operation_0320
feature list: operation_0474
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Yi He

GlyMDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0154
application sub category: topic_0203
application sub category: topic 3518
citation: btz934
citation: pmcid:PMC7178435
citation: pubmed:31841142
description: Glycan Microarray Database and Analysis Toolset.
feature list: operation 2421
feature list: operation 2426
feature list: operation 2495

GlycanAnalyzer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic 3068
application sub category: topic 3520
author: Dr. Ian Walsh
citation: bty681
citation: pmcid:PMC6378934
citation: pubmed:30101321
description: Software for automated interpretation of N -glycan profiles after exoglycosidase digestions.
feature list: operation 3215
feature list: operation 3627
feature list: operation 3633
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.action
software help: tutorial.action
primary contact: Dr. Christopher H. Taron
primary contact: Dr. Ian Walsh
primary contact: Prof. Pauline M. Rudd

GlycanFormatConverter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0108
application sub category: topic_0152
application sub category: topic_0154
citation: bty990
citation: pmcid:PMC6612873
citation: pubmed:30535258
description: Conversion tool for translating the complexities of glycans.
is accessible for free: true
license: GPL-2.0
operating system: Mac

Glyco-DIA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0121
application sub category: topic 2815
application sub category: topic 3520
citation: S41592-019-0504-X
citation: pubmed:31384044
description: a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries | Glyco-DIA is a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries | The Glyco-DIA library consists of sublibraries obtained from human cell lines and human serum, and it currently covers 2,076 O-glycoproteins (11,452 unique glycopeptide sequences) and the five most common core1 O-glycan structures. Applying the Glyco-DIA library to human serum without enrichment for glycopeptides enabled us to identify and quantify 269 distinct glycopeptide sequences bearing up to 5 different core1 O-glycans from 159 glycoproteins in a singleshot analysis. The DIA method is expandable and widely applicable to different glycoproteomes, and it may represent a first step towards direct and comprehensive approach to glycoproteomics
feature list: operation_0417
feature list: operation 3501
feature list: operation 3799

Glycosylator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0152
application sub category: topic_0166
application sub category: topic_0176
application sub category: topic 3300
citation: S12859-019-3097-6
citation: pmcid:PMC6806574
citation: pubmed:31640540
description: a Python framework for the rapid modeling of glycans. Framework for the rapid modeling glycans and glycoproteins. Glycosylator is a Python framework for the identification, modeling and modification of glycans in protein structure. It can be used directly in a Python script through its API or through its Graphical User Interface (GUI). The GUI provides a straightforward 2D rendering of a glycoprotein that allows for a quick visual inspection of the gylcosylation state of all the sequons on a protein structure. Modeled glycans can be further refined by a genetic algorithm for removing clashes and sampling alternative conformations. Glycosylator can also identify specific 3D glycans on a protein structure using a library of predefined templates. Glycosylator has been implemented in a generic way allowing the user to expand the library to incorporate other polymers
feature list: operation_0337
feature list: operation_0417
feature list: operation 2476
feature list: operation 3192

GmT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3174
application sub category: topic 3382
application sub category: topic 3697
citation: giy166
citation: pmcid:PMC6377400
citation: pubmed:30597007
description: Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur.
feature list: operation 3192
feature list: operation 3431
feature list: operation 3797
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: metagenomics
primary contact: Saskia Hiltemann

Gmove
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0622
application sub category: topic 3170
description: Gmove is a genome annotation tool. This combiner takes as input mapping of RNA-seq or protein or ab initio data.
feature list: operation_0362
feature list: operation 2454
is accessible for free: true

GoldenMutagenesis
type: SoftwareApplication
input: Sequence variations
  type: FormalParameter
  additional type: data 3498
  encoding format: format 1915
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 2200
input: Sequence trace
  type: FormalParameter
  additional type: data_0924
  encoding format: format 3000
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 2200
output: Protocol
  type: FormalParameter
  additional type: data 2531
  encoding format: format 3508
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 3603
output: PCR primers
  type: FormalParameter
  additional type: data 1240
  encoding format: format 2330
  encoding format: format 2331
  encoding format: format 3508
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web application
application sub category: topic_0091
application sub category: topic_0196
application sub category: topic_0601
application sub category: topic_0632
application sub category: topic 2533
application sub category: topic 3361
application sub category: topic 3895
author: https://orcid.org/0000-0001-5444-9282
citation: s41598-019-47376-1
citation: https://doi.org/10.1101/453621
citation: pmcid:PMC6662682
citation: pubmed:31358887
contributor: https://orcid.org/0000-0002-9212-9957
description: The Golden Gate cloning technique has been proven to be a highly efficient toolbox for a variety of cloning setups. Based on its modular concept it is particularly suitable for the use in multiple-site mutagenesis approaches. In this technical note we developed a protocol termed Golden Mutagenesis for the rapid, easy, reliable and cheap formation of mutagenesis libraries. One to five positions could be altered in parallel or simultaneously within two days. To facilitate the implementation of this technique, this R-library has been developed for the automated primer design and the graphical evaluation of sequencing results to determine the quality of the library.
feature list: operation_0308
feature list: operation 3675
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.1.1

GpABC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 2269
citation: https://doi.org/10.1101/769299
description: a Julia package for approximate Bayesian computation with Gaussian process emulation | GpABC provides algorithms for likelihood - free parameter inference and model selection using Approximate Bayesian Computation (ABC). Two sets of algorithms are available:
feature list: operation 3659
license: MIT

Gplas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0769
application sub category: topic 3305
application sub category: topic 3673
author: Sergio Arredondo-Alonso
citation: btaa233
citation: https://doi.org/10.1101/2020.07.21.20158808
citation: https://doi.org/10.1101/835900
citation: s13073-020-00825-3
citation: pmcid:PMC7320608
citation: pmcid:PMC7816424
citation: pubmed:32271863
citation: pubmed:33472670
description: A comprehensive tool for plasmid analysis using short-read graphs. gplas: Binning plasmid-predicted contigs using short-read graphs
feature list: operation_0524
feature list: operation_0525
license: GPL-3.0
software help: README.md
software version: V0.6.0
software version: V0.7.0

GrapeMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: An integrated database for grapevine data
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 1.0

GraphAligner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0199
application sub category: topic_0625
citation: https://doi.org/10.1101/810812
description: Rapid and Versatile Sequence-to-Graph Alignment. Seed-and-extend program for aligning long error-prone reads to genome graphs. For a description of the bitvector alignment extension algorithm, see https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz162/5372677.
feature list: operation_0524
feature list: operation 3182
feature list: operation 3196
feature list: operation 3198
feature list: operation 3211
license: MIT

GraphClust2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
application sub category: topic_0097
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3794
citation: GIZ150
citation: pmcid:PMC6897289
citation: pubmed:31808801
description: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. A pipeline for structural clustering of RNA secondary structures. GraphClust2 is a workflow for scalable clustering of RNAs based on sequence and secondary structures feature. GraphClust2 is implemented within the Galaxy framework and consists a set of integrated Galaxy tools and flavors of the linear-time clustering workflow.
feature list: operation_0278
feature list: operation_0302
feature list: operation_0502
feature list: operation 3432
license: GPL-3.0

Graph Peak Caller
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0749
application sub category: topic 3169
citation: journal.pcbi.1006731
citation: pmcid:PMC6396939
citation: pubmed:30779737
description: Tool for calling transcription factor peaks on graph-based reference genomes using ChIP-seq data.
feature list: operation_0487
feature list: operation 3215
feature list: operation 3222
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
primary contact: Biomedical Informatics Research Group (BMI)

Graphmap2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3512
citation: https://doi.org/10.1101/720458
description: Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 | GraphMap2 - A highly sensitive and accurate mapper for long, error-prone reads | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and | GSNAP: Genomic Short-read Nucleotide Alignment Program | Links are provided below in parentheses for users who wish to download the files with a command-line tool, like wget
feature list: operation_0526
feature list: operation 3192
feature list: operation 3198
license: MIT

Graphtyper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3168
citation: ng.3964
citation: pubmed:28945251
description: Publicly available novel algorithm and software for discovering and genotyping sequence variants.
feature list: operation_0484
feature list: operation 3196
feature list: operation 3227
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Hannes Pétur Eggertsson

GreatSPN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
application sub category: topic 3318
application sub category: topic 3334
application sub category: topic 3375
citation: S12859-019-3196-4
citation: pmcid:PMC6904991
citation: pubmed:31822261
description: A computational approach based on the colored Petri net formalism for studying multiple sclerosis. BACKGROUND:Multiple Sclerosis (MS) is an immune-mediated inflammatory disease of the Central Nervous System (CNS) which damages the myelin sheath enveloping nerve cells thus causing severe physical disability in patients. Relapsing Remitting Multiple Sclerosis (RRMS) is one of the most common form of MS in adults and is characterized by a series of neurologic symptoms, followed by periods of remission. Recently, many treatments were proposed and studied to contrast the RRMS progression. Among these drugs, daclizumab (commercial name Zinbryta), an antibody tailored against the Interleukin-2 receptor of T cells, exhibited promising results, but its efficacy was accompanied by an increased frequency of serious adverse events.
feature list: operation 3359

Green listed
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0632
citation: btw739
description: Web-based tool that rapidly designs custom CRISPR screens targeting sets of genes defined by the user.
feature list: operation 3096
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: green-listed
primary contact: Fredrik Wermeling

GripDL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic 3382
citation: JOURNAL.PCBI.1007324
citation: pmcid:PMC6764701
citation: pubmed:31527870
description: Predicting gene regulatory interactions based on spatial gene expression data and deep learning | Gene regulatory interaction prediction through Deep Learning | Gene regulatory interaction prediction through Deep Learning By Qingwei Fang, 2018
feature list: operation_0277
feature list: operation 1781
feature list: operation 3439

GrowthEstimate
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3390
application sub category: topic 3474
citation: JOURNAL.PONE.0216030
citation: pmcid:PMC6713322
citation: pubmed:31461459
description: A model for studying living resources through digestive efficiency | The neural computational model GrowthEstimate is introduced with focusing on new perspectives for the practical estimation of weight specific growth rate (SGR, % day-1). It is developed using recurrent neural networks of reservoir computing type, for estimating SGR based on the known data of three key biological factors relating to growth

GsVec
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0203
application sub category: topic_0218
application sub category: topic_0602
application sub category: topic 3518
citation: https://doi.org/10.1101/846691
description: Comprehensive biological interpretation of gene signatures using semantic distributed representation. GsVec (Gene signature Vector) is an analysis method that supports the biological interpretation of Gene signature obtained by gene expression analysis of Bioinformatics. The association between the gene signature to be interpreted and the gene signature of the Pathway / Gene Ontology data base is performed by natural language processing
feature list: operation_0277
feature list: operation 2436
feature list: operation 3891
license: GPL-2.0

Gypsum-DL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2275
application sub category: topic 3343
application sub category: topic 3369
citation: S13321-019-0358-3
citation: pmcid:PMC6534830
citation: pubmed:31127411
description: Program for preparing small-molecule libraries for structure-based virtual screening.
feature list: operation_0482
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: https://orcid.org/0000-0002-5808-4097

H3ABioNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic_0769
application sub category: topic 3053
citation: AASOPENRES.12847.2
description: The ML Glossary developed by H3ABioNet The machine learning glossary for Bioinformaticians | Ready to get started? Build your own site from scratch or generate one for your project | Code repository for the RefGraph project
feature list: operation 3431
feature list: operation 3557
feature list: operation 3891

HAF-pipe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3056
application sub category: topic 3168
citation: G3.119.400755
citation: pmcid:PMC6893198
citation: pubmed:31636085
description: Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments. calculate haplotype-derived allele frequencies for pool-seq samples. HAF-pipe is a bash- and R-based pipeline to calculate haplotype-inferred allele frequencies from pool-seq data and founder SNP profiles. To simulate recombination and pooled sequencing data from a panel of sequenced founders, see the scripts HAFpipe-sim.run_forqs.sh and HAFpipe-sim.simulate_poolseq.sh in the simulations folder
feature list: operation_0484
feature list: operation_0487
feature list: operation 3196
feature list: operation 3557

HAMR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
additional type: Web service
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3512
citation: 978-1-4939-8808-2 4
citation: pubmed:30539546
description: HAMR (High-throughput Annotation of Modified Ribonucleotides) - web application that allows you to detect and classify modified nucleotides in RNA-seq data.
feature list: operation_0484
feature list: operation 3185
feature list: operation 3196
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: hamr
software help: README.md
software version: 1.2

HCCPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3360
citation: https://doi.org/10.1101/758250
description: Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma using Large-scale Transcriptomics Data | A webserver to predict Hepatocellular carcinoma (HCC) | Pipeline Differential Expression Analysis | HCCpred is a web-bench for the prediction of tumorous and non-tumorous Hepatocellular Carcinoma (HCC) patients. Our major prediction modules based on the robust biomarkers such as 3-Gene HCC Biomarker, 4-Gene HCC Biomarker, 5-Gene HCC Biomarker. These HCC biomarkers identified using gene expression profiles of a total of 3,961 samples include 2,306 HCC and 1,655 non-tumorous samples. The datasets derived from various profiling platforms such as Affymatrix, Illumina, High-througput and Agilent. The user can also analyse the expression pattern of any of 26 "core genes of HCC" in cancerous vs normal conditions
feature list: operation_0313
feature list: operation 3223
feature list: operation 3501

HD-BET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3474
citation: hbm.24750
citation: pmcid:PMC6865732
citation: pubmed:31403237
description: Automated brain extraction of multisequence MRI using artificial neural networks | Brain extraction is a critical preprocessing step in the analysis of neuroimaging studies conducted with magnetic resonance imaging (MRI) and influences the accuracy of downstream analyses. The majority of brain extraction algorithms are, however, optimized for processing healthy brains and thus frequently fail in the presence of pathologically altered brain or when applied to heterogeneous MRI datasets. Here we introduce a new, rigorously validated algorithm (termed HD-BET) relying on artificial neural networks that aim to overcome these limitations

HD-GMCM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3577
citation: BTZ599
citation: pubmed:31368480
description: Gaussian Mixture Copulas for High-Dimensional Clustering and Dependency-based Subtyping | MOTIVATION:The identification of sub-populations of patients with similar characteristics, called patient subtyping, is important for realizing the goals of Precision Medicine. Accurate subtyping is crucial for tailoring therapeutic strategies that can potentially lead to reduced mortality and morbidity. Model-based clustering, such as Gaussian mixture models, provides a principled and interpretable methodology that is widely used to identify subtypes. However, they impose identical marginal distributions on each variable; such assumptions restrict their modeling flexibility and deteriorates clustering performance. RESULTS:In this paper, we use the statistical framework of copulas to decouple the modeling of marginals from the dependencies between them. Current copula-based methods cannot scale to high dimensions due to challenges in parameter inference
feature list: operation 3891

HDCytoData
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
citation: F1000RESEARCH.20210.1
description: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats | Data package containing high-dimensional cytometry data sets in SummarizedExperiment and flowSet formats | R code to reproduce example in Figure 1 in our HDCytoData paper | The HDCytoData package is an extensible resource containing a set of publicly available high-dimensional flow cytometry and mass cytometry (CyTOF) benchmark datasets, which have been formatted into SummarizedExperiment and flowSet Bioconductor object formats. The data objects are hosted on Bioconductor's ExperimentHub platform
feature list: operation_0335
feature list: operation 2422
feature list: operation 3891
license: MIT
software help: HDCytoData-example

HEGIAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3295
citation: bbz072
citation: pmcid:PMC7373178
citation: pubmed:31504171
description: New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform | Essential genes are those whose loss of function compromises organism viability or results in profound loss of fitness. Recent gene-editing technologies have provided new opportunities to characterize essential genes. Here, we present an integrated analysis that comprehensively and systematically elucidates the genetic and regulatory characteristics of human essential genes. First, we found that essential genes act as 'hubs' in protein-protein interaction networks, chromatin structure and epigenetic modification. Second, essential genes represent conserved biological processes across species, although gene essentiality changes differently among species. Third, essential genes are important for cell development due to their discriminate transcription activity in embryo development and oncogenesis
feature list: operation_0277
feature list: operation 2495
feature list: operation 3439

HERMES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic_0749
application sub category: topic 3384
citation: JBHI.2018.2824312
citation: pubmed:29993993
description: Aims to bring together geographically dispersed medical personnel in order to share a common workspace where they can collaborate over medical images in real-time.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

HHypermap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0218
application sub category: topic_0621
citation: PEERJ.PREPRINTS.2238V6
citation: PEERJ.PREPRINTS.2238V7
description: Implementing an open source spatio-temporal search platform for Spatial Data Infrastructures. Hypermap Registry, remote map services made easy for your SDI. Hypermap Registry is a platform that manages OWS, Esri REST, and other types of map service harvesting, and orchestration and maintains uptime statistics for services and layers. Check Hypermap Registry documentation.
feature list: operation 2421
feature list: operation 2429
feature list: operation 3760
feature list: operation 3891
license: MIT

HIO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic_0749
application sub category: topic 3305
citation: genes10120960
citation: pmcid:PMC6947307
citation: pubmed:31766582
description: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research. The Hearing Impairment Ontology (HIO) is a collaboratively developed resource by a group of experts in different aspects of hearing impairment (HI) to provide a common controlled HI terminology and concepts. The HIO will allow researchers and clinicians alike to readily access standardised HI-related knowledge in a single location and promote collaborations and HI information sharing, including epidemiological, socio-environmental, biomedical, genetic and phenotypic information. It is worth noting, this ontology provides an illustration of the adaptability of the Sickle Cell Disease Ontology framework for use in developing a disease-specific ontology.
feature list: operation 2422
feature list: operation 3559
license: GPL-3.0

HIRAC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic_0654
application sub category: topic 3382
citation: https://doi.org/10.1101/863803
description: Inferring Chromosome Radial Organization from Hi-C Data. The included Python scripts (mat2net.py, and predictCTpos.py) contain an implemention of the HIRAC computational technique described in the following manuscript.
feature list: operation 3659
license: GPL-3.0

HIV-1
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0199
application sub category: topic_0781
application sub category: topic_0804
application sub category: topic 3324
application sub category: topic 3400
citation: https://doi.org/10.1101/804781
description: Detection of novel HIV-1 drug resistance mutations by support vector analysis of deep sequence data and experimental validation. The HIV Databases cover HIV sequences, HIV molecular immunology, HIV drug resistance mutations and nonhuman primate HIV/SIV vaccine trials. Each of these topics are available through a dedicated database, extensively annotated and with many specialized search and analysis tools. The HIV databases are supported by the NIH and DOE and maintained at the Los Alamos National Laboratory. The HIV databases contain comprehensive data on HIV genetic sequences and immunological epitopes.
feature list: operation 2421
feature list: operation 3202
feature list: operation 3557

HIV-ASSIST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0781
application sub category: topic 3068
application sub category: topic 3315
application sub category: topic 3379
citation: qai.0000000000002118
citation: pubmed:31513553
description: Online, Educational, Clinical Decision Support Tool to Guide Patient-Centered ARV Regimen Selection | HIV-ASSIST (HIV Antiretroviral Selection Support and Interactive Search Tool) is a web-based platform designed at Johns Hopkins University to assist and educate clinicians in personalizing ART regimens for their patients | HIV-ASSIST is an online, interactive, educational tool to inform clinical decision-making for ARV selection
feature list: operation 2428
feature list: operation 3196
feature list: operation 3436
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

HIV-DRLink
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0804
application sub category: topic 3168
application sub category: topic 3379
citation: https://doi.org/10.1101/866715
description: A tool for detecting linked HIV-1 drug resistance mutations in next generation sequencing data. A script detect and calculate Linked HIV drug resistant mutations on single HIV genomes. HIV-DRLink_github.pl is a script that detects and calculates Linked HIV drug resistant mutations on single HIV genomes. The HIV Databases cover HIV sequences, HIV molecular immunology, HIV drug resistance mutations and nonhuman primate HIV SIV vaccine trials. The HIV databases contain comprehensive data on HIV genetic sequences and immunological epitopes
feature list: operation 1812
feature list: operation 2421
feature list: operation 3202
feature list: operation 3482

HIV-related
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0602
application sub category: topic 2269
application sub category: topic 3305
citation: S12889-019-7681-5
citation: pmcid:PMC6849208
citation: pubmed:31718603
description: Optimal allocation of HIV resources among geographical regions.
feature list: operation 2426

HIVCoR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic 3474
citation: J.COMPBIOLCHEM.2019.05.006
citation: pubmed:31146118
description: Web server for predicting HIV-1 CRF01_AE coreceptor usage.
feature list: operation 3196
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: hivcor
primary contact: Watshara Shoombuatong

HIrisPlex-S
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0625
application sub category: topic 2885
citation: J.FSIGEN.2019.102152
citation: pubmed:31518964
description: Massively parallel sequencing solutions for two common forensically used platforms | HIrisPlex-S Eye, Hair and Skin Colour DNA Phenotyping Webtool | 8px 9px 10px 11px 12px 13px 14px 15px 16px 17px 18px | With the advancement of DNA phenotyping as a tool in Forensic and Anthropological usage, we now provide an easy to use interactive website to predict eye, hair and skin colour from DNA using the IrisPlex, HIrisPlex and HIrisPlex-S systems
feature list: operation 3196
feature list: operation 3894

HKPocket
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3336
application sub category: topic 3373
citation: S12859-019-3254-Y
citation: pmcid:PMC6884818
citation: pubmed:31783725
description: Human kinase pocket database for drug design. BACKGROUND:The kinase pocket structural information is important for drug discovery targeting cancer or other diseases. Although some kinase sequence, structure or drug databases have been developed, the databases cannot be directly used in the kinase drug study. Therefore, a comprehensive database of human kinase protein pockets is urgently needed to be developed. RESULTS:Here, we have developed HKPocket, a comprehensive Human Kinase Pocket database. This database provides sequence, structure, hydrophilic-hydrophobic, critical interactions, and druggability information including 1717 pockets from 255 kinases. We further divided these pockets into 91 pocket clusters using structural and position features in each kinase group. The pocket structural information would be useful for preliminary drug screening
feature list: operation_0321
feature list: operation_0337
feature list: operation 2421

HLA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: 978-1-4939-9773-2 12
citation: pubmed:31502156
description: Using RNA Sequencing to Characterize the Tumor Microenvironment | Using k-mers to call HLA alleles in RNA sequencing data | HLAProfiler uses the k-mer content of next generation sequencing reads to call HLA types in a sample. Based on the k-mer content each each read pair is assigned to an HLA gene and the aggregate k-mer profile for the gene is compared to reference k-mer profiles to determin the HLA type. Currently HLAProfiler only supports paired-end RNA-seq data
feature list: operation 2495
feature list: operation 3630
feature list: operation 3800

HLA Ligand Atlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic 2830
application sub category: topic 3421
citation: https://doi.org/10.1101/778944
description: The HLA Ligand Atlas. A resource of natural HLA ligands presented on benign tissues | The HLA Ligand Atlas is a comprehensive, tissue and HLA allele specific collection of HLA ligands, generated from more than 1,000 MS experiments | This website uses cookies to ensure you get the best experience on our website. Learn more | Warning The HLA Ligand Atlas is currently in a beta test phase . Please notice that the data and interface design might undergo frequent changes. You are welcome to contact us at
feature list: operation 3891
feature list: operation 3893

HLMethy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0203
application sub category: topic 3474
citation: S11103-019-00930-X
citation: pubmed:31722090
description: A machine learning-based model to identify the hidden labels of m6A candidates. HLMethy: Machine learning-based model to identify the hidden labels of candidate m6A modifications
feature list: operation 3222
feature list: operation 3435

HMMER2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web application
application sub category: topic_0160
description: Older version of the HMMER3 program (https://bio.tools/hmmer3) used for searching sequence databases for sequence homologs, and for making sequence alignments.
feature list: operation 2421
feature list: operation 3092
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: Userguide.pdf
software version: 2.1.1 - 2.4i

HMP2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0634
application sub category: topic_0804
application sub category: topic 3697
citation: S41586-019-1237-9
citation: pmcid:PMC6650278
citation: pubmed:31142855
description: Collection of workflows that handle processing several different data types assocaited with the IBDMDB (Inflammatory Bowel Disease Multi’omics Database) project.
feature list: operation 3192
feature list: operation 3629
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Curtis Huttenhower
primary contact: Ramnik J. Xavier

HNADOCK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0097
application sub category: topic_0099
application sub category: topic 2275
citation: GKZ412
citation: pmcid:PMC6602492
citation: pubmed:31114906
description: Nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures.
feature list: operation_0278
feature list: operation_0279
feature list: operation 3899
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
primary contact: Lab of Bioinformatics and Molecular Modeling
primary contact: Sheng-You Huang
primary contact: Yi Xiao

HNCDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0209
application sub category: topic 2640
application sub category: topic 3406
citation: FONC.2019.00371
citation: pmcid:PMC6527845
citation: pubmed:31139565
description: Integrated Gene and Drug Database for Head and Neck Cancer.
feature list: operation_0306
feature list: operation 3223
feature list: operation 3463
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Ankui Yang
primary contact: Xiaoqing Pei
primary contact: Zhixiang Zuo

HNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3304
application sub category: topic 3306
citation: https://doi.org/10.1101/740597
description: A new software tool for interpreting the cellular and network origin of human MEG/EEG data | The Human Neocortical Neurosolver (HNN) is a software tool that gives researchers/clinicians the ability to develop/test hypotheses on circuit mechanisms underlying EEG/MEG data | Click here to join our Google Group | Human Neocortical Neurosolver (HNN) is a user-friendly software tool that provides a novel solution to this challenge | Electro- and magneto-encephalography (EEG MEG) are among the most powerful technologies to non-invasively record human brain activity with millisecond resolution
feature list: operation 3891

HOME
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3674
citation: S12859-019-2845-Y
citation: pmcid:PMC6521357
citation: pubmed:31096906
description: HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification.
feature list: operation 3186
feature list: operation 3206
feature list: operation 3207
is accessible for free: true
operating system: Linux
software help: README.md
primary contact: https://orcid.org/0000-0001-6637-7239

HOPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic_0749
application sub category: topic 3337
application sub category: topic 3517
citation: S13059-019-1844-7
citation: pmcid:PMC6815001
citation: pubmed:31653226
description: A quantitative score reveals pervasive horizontal pleiotropy in human genetic variation is driven by extreme polygenicity of human traits and diseases. Allows to compute the HOrizontal Pleiotropy Score (HOPS) from summary statistics. HOPS (HOrizontal Pleiotropy Score). The HOPS package allows to compute the horizontal pleiotropy score (HOrizontal Pleiotropy Score) from summary statistics. The package includes a shiny visualization tool to visualize and download the full set of HOPS results computed using UK Biobank summary statistics
feature list: operation_0282
feature list: operation 3196
feature list: operation 3791
feature list: operation 3799
license: GPL-3.0

HOT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3674
citation: GKZ460
citation: pmcid:PMC6582337
citation: pubmed:31114922
description: Examining the basis of high-occupancy target regions.
feature list: operation_0417
feature list: operation_0445
feature list: operation 3207
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-0468-0117
primary contact: Verdan Franske

HPAanalyze
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic 3308
application sub category: topic 3382
citation: S12859-019-3059-Z
citation: pmcid:PMC6734269
citation: pubmed:31500569
description: An R package that facilitates the retrieval and analysis of the Human Protein Atlas data | To access this site please go to: http://alexdussaq.info/jsHPAanalyze | A Bioconductor package to retrieve and analyze data from the Human Protein Atlas | Results: HPAanalyze is an R package for retreiving and performing exploratory data analysis from HPA. It provides functionality for importing data tables and xml files from HPA, exporting and visualizing data, as well as download all staining images of interest. The package is free, open source, and available via Github | Background: The Human Protein Atlas program aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics
feature list: operation 2422
feature list: operation 2495
license: GPL-3.0

HPCCS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 3047
application sub category: topic 3314
application sub category: topic 3520
citation: 978-1-0716-0030-6 19
citation: pubmed:31729669
description: Collision Cross Section Calculations Using HPCCS. The High Performance Collision Cross Section (HPCCS) is a new software for fast and accurate calculation of CCS for molecular ions. Based on the Trajectory Method (TM), HPCCS was parallelized and optimized to be an user-friendly program. High Performance Collision Cross Section Calculation – HPCCS
feature list: operation_0302
feature list: operation 2476
feature list: operation 3359

HPO2GO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0128
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic_0634
citation: PEERJ.PREPRINTS.26663V2
description: Prediction of human phenotype ontology term associations using cross ontology annotation co-occurrences. Mapping between HPO and GO terms. If you find HPO2GO useful, please consider citing this publication:. Mapping between Human Phenotype Ontology (HPO) and Gene Ontology (GO) terms for the prediction of gene/protein - function - phenotype - disease associations. In this study, a novel approach is proposed for the identification of relationships between biomedical entities by automatically mapping phenotypic abnormality defining HPO terms with biomolecular function defining GO terms, where each association indicates the occurrence of the abnormality due to the loss of the biomolecular function expressed by the corresponding GO term
feature list: operation 1777
feature list: operation 2429
feature list: operation 3280
license: GPL-3.0

Helix Positioner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic 2830
application sub category: topic 3534
citation: J.CSBJ.2019.11.001
citation: pmcid:PMC6872852
citation: pubmed:31768230
description: Discovery of novel helix binding sites at protein-protein interfaces. Helix Positioner a program for locating helix binding sites at protien-protein interfaces.
feature list: operation 2464
feature list: operation 2476
feature list: operation 2492

Human Proteoform Atlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
application sub category: topic_0080
application sub category: topic_0089
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic 3320
citation: GKAB1086
citation: pmcid:PMC8728143
citation: pubmed:34986596
description: The Human Proteoform Atlas (HPfA) is a web-based repository of experimentally verified human proteoforms and is a direct descendant of the Consortium of Top-Down Proteomics' (CTDP) Proteoform Atlas
feature list: operation_0224
feature list: operation_0417
feature list: operation 3755
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: api

HRMAn
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0769
application sub category: topic 3382
application sub category: topic 3474
citation: 978-1-4939-9857-9 21
citation: pubmed:31758464
description: Image-Based Quantitation of Host Cell-Toxoplasma gondii Interplay Using HRMAn. Host Response to Microbe Analysis. HRMAn enables you to automatically analyse parameters of host-pathogen interaction derived from immunofluorescent experiments
feature list: operation 3431
feature list: operation 3443
feature list: operation 3799

HSIC Lasso
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3360
application sub category: topic 3517
application sub category: topic 3518
citation: BTZ333
citation: pmcid:PMC6612810
citation: pubmed:31510671
description: Model-free biomarker detection for ultra-high dimensional data | Versatile Nonlinear Feature Selection Algorithm for High-dimensional Data | Supervised, nonlinear feature selection method for high-dimensional datasets | pyHSICLasso is a package of the Hilbert Schmidt Independence Criterion Lasso (HSIC Lasso), which is a black box (nonlinear) feature selection method considering the nonlinear input and output relationship. HSIC Lasso can be regarded as a convex variant of widely used minimum redundancy maximum relevance (mRMR) feature selection algorithm | pyHSICLasso is a package of the Hilbert Schmidt Independence Criterion Lasso (HSIC Lasso), which is a nonlinear feature selection method considering the nonlinear input and output relationship
feature list: operation 3196
feature list: operation 3557
feature list: operation 3659
license: MIT

HSMRF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic 2269
application sub category: topic 3305
application sub category: topic 3324
citation: https://doi.org/10.1101/853960
description: Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts. Code for our work developing and characterizing the HSMRF priors for birth-death processes. This repository contains code for analyses from "Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts" (Magee et al. 2019). In the directory 1_simulation_study is code for simulating a number of trees under a time-dependent birth-death process, inferring diversification rates under the HSMRF-based and GMRF-based models, and processing those results. In the directory 2_empirical_analyses is code for the empirical analyses presented in the manuscript. Both directories contain more extensive readme files.
feature list: operation_0324
feature list: operation 2426
feature list: operation 3658

HTRgene
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3518
citation: S12859-019-3072-2
citation: pmcid:PMC6886170
citation: pubmed:31787073
description: A computational method to perform the integrated analysis of multiple heterogeneous time-series data. This program was designed for integrating analysis of multiple heterogeneous time-series gene expression data to identify response genes.
feature list: operation_0277
feature list: operation 2495
feature list: operation 3223

HULK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: s40168-019-0653-2
citation: pmcid:PMC6420756
citation: pubmed:30878035
description: Histosketching Using Little Kmers (HULK) - tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.
feature list: operation 3435
feature list: operation 3472
feature list: operation 3798
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Will Rowe

HUPAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0196
application sub category: topic 3170
application sub category: topic 3673
citation: S13059-019-1751-Y
citation: pmcid:PMC6670167
citation: pubmed:31366358
description: A pan-genome analysis pipeline for human genomes | Human pan-genome analysis pipeline | HUman PAN-genome analysis toolkit | The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. It encourages us to build the pan-genome of human population. Previously, our team developed a "map-to-pan" strategy, EUPAN, specific for eukaryotic pan-genome analysis. However, due to the large genome size of individual human genome, EUPAN is not suit for pan-genome analysis involving in hundreds of individual genomes. Here, we present an improved tool, HUPAN (HUman Pan-genome ANalysis), for human pan-genome analysis | The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions | We propose HUPAN strategy primarily in the 185 deep sequencing and 90 assembled Han Chinese genomes
feature list: operation_0523
feature list: operation_0525
feature list: operation 3216

HaGiS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0634
application sub category: topic_0780
application sub category: topic 3810
citation: MPMI-07-19-0180-A
citation: pubmed:31415224
description: R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean | Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity | Analysis of plant pathogen pathotype survey data. Functions provided calculate distribution of susceptibilities, distribution of complexities with statistics, pathotype frequency distribution, as well as diversity indices for pathotypes. This package is meant to be a direct replacement for Herrmann, Löwer, Schachtel's (1999) <doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS', previously used for pathotype analysis | The goal of hagis is to provide analysis tools for plant pathogens with gene-for-gene interactions in the R programming language that the original Habgood-Gilmour Spreadsheet, HaGiS, (Herrmann, Löwer and Schachtel) provided
feature list: operation_0337
feature list: operation 3461
license: MIT

HaTSPiL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 3168
application sub category: topic 3372
citation: JOURNAL.PONE.0222512
citation: pmcid:PMC6793853
citation: pubmed:31613890
description: A modular pipeline for high-throughput sequencing data analysis. High-throughput sequencing pipeline software. HaTSPiL is a a Python pipeline for High-Throughput Sequencing analysis. It has been designed to be used inside our laboratory, the Salvatore Oliviero lab within the HuGef institute, TO (IT). Whoever find it useful or a good starting point to develop his own pipeline is encouraged to use and hack the code
feature list: operation 3192
feature list: operation 3200
feature list: operation 3359
feature list: operation 3454
license: MIT

Haloarchaeal Genomes
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0749
application sub category: topic 3295
application sub category: topic 3518
citation: https://doi.org/10.1186/1746-1448-6-12
citation: pmcid:PMC3023673
citation: pubmed:21192823
description: Haloarchaeal genomes database.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: haloweb.pl
primary contact: Shiladitya DasSarma

Haplin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3517
citation: s12859-019-2727-3
citation: pmcid:PMC6444579
citation: pubmed:30940094
description: R package for power and sample size calculations in genetic association analyses of family triads and unrelated controls.
feature list: operation_0487
feature list: operation 3196
feature list: operation 3454
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Haplin
software version: 7.1.0
primary contact: Hakon K. Gjessing

HaploReg
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 2885
citation: gkr917
citation: pmcid:PMC3245002
citation: pubmed:22064851
description: Association between DIO2 polymorphism and the risk of Kashin-Beck disease in the Tibetan population | HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with chromatin state and protein binding annotation from the Roadmap Epigenomics and ENCODE projects, sequence conservation across mammals, the effect of SNPs on regulatory motifs, and the effect of SNPs on expression from eQTL studies. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation
feature list: operation_0484
feature list: operation_0487
feature list: operation 3196

HaploTypo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0769
citation: btz933
citation: pmcid:PMC7178392
citation: pubmed:31834373
description: a variant-calling pipeline for phased genomes. This is the Haplotypo repository. This repository contains the Haplotypo pipeline. HaploTypo is a pipeline suited to map variants into haplotypes in genetic variation analyses. After mapping and variant calling on a phased reference genome, HaploTypo infers the haplotype correspondence for each heterozygous variant. It also generates two independent FASTA files for each reconstructed haplotype
feature list: operation_0487
feature list: operation 3227
feature list: operation 3454

Haploscope
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic 3056
application sub category: topic 3305
citation: gepi.20640
citation: pmcid:PMC3725725
citation: pubmed:22147662
description: Tool for visualizing haplotype diversity, based on a cluster-based model for haplotype variation
feature list: operation_0487
feature list: operation_0488
feature list: operation 3432
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Haploscope Manual.pdf
software version: 0.4.1
primary contact: Paul Scheet

HashClone
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3063
author: Francesca Cordero
author: Marco Becc
citation: s12859-017-1923-2
citation: pmcid:PMC5701356
citation: pubmed:29169317
description: it is an easy-to-use and reliable bioinformatics tool that provides B-cells clonality assessment and MRD monitoring over time analyzing data from Next-Generation Sequencing (NGS) technique. The HashClone strategy-based is composed of three steps: the first and second steps implement an alignment-free prediction method that identifies a set of putative clones belonging to the repertoire of the patient under study. In the third step the IGH variable region, diversity region, and joining region identification is obtained by the alignment of rearrangements with respect to the international ImMunoGenetics information system database.
is accessible for free: true
license: GPL-3.0
operating system: Linux
software version: version 1.2
primary contact: Raffaele Calogero

Hass
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 2885
application sub category: topic 3810
citation: S41598-019-56526-4
citation: pmcid:PMC6934854
citation: pubmed:31882769
description: Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.). This is a repository for a analysis of avocado GBS data in R. This is a repository for a analysis of GBS data in R. The R packages used in this repository are shown below:.
feature list: operation_0484
feature list: operation 3196
feature list: operation 3227

HastaLaVista
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3344
application sub category: topic 3407
application sub category: topic 3421
citation: s13321-019-0399-7
citation: pmcid:PMC6896291
citation: pubmed:33430999
description: Web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences. R package that provide interactive graphical interface for metabolic profiling. If you find it useful, please cite this work. to convert R variables into a JSON object and save it as a file. hastaLaVista is developed and tested using Chrome, although it is known to work with other browser. In the case that a feature is not working as expected please try using Chrome before filling an issue
feature list: operation_0337
feature list: operation 3214
feature list: operation 3557
feature list: operation 3891
license: MIT

HawkDock
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0128
application sub category: topic_0749
application sub category: topic 2275
citation: GKZ397
citation: pmcid:PMC6602443
citation: pubmed:31106357
description: Web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.
feature list: operation_0482
feature list: operation 2492
feature list: operation 3899
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: Gaoqi Weng
primary contact: Tingjun Hou

Hayai-Annotation Plants
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0637
application sub category: topic_0780
application sub category: topic_0821
citation: btz380
citation: pmcid:PMC6821316
citation: pubmed:31093654
description: R package for an Ultra-Fast and Comprehensive Gene Annotation in Plants.
feature list: operation_0224
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Andrea Ghelfi

HetEnc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3474
citation: S12864-019-5997-2
citation: pmcid:PMC6686264
citation: pubmed:31395005
description: A deep learning predictive model for multi-type biological dataset | HetEncs: A Deep Learning Classifier for Integrated Gene Expression Analysis
feature list: operation 2495
feature list: operation 2939
feature list: operation 3891

HeveaDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic 3168
application sub category: topic 3321
citation: https://doi.org/10.1101/708305
description: A genetic resource database for rubber tree genomic study | Molecular & Genetic Resources for Hevea tree
feature list: operation 3216
feature list: operation 3431
feature list: operation 3766

HiCBricks
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0091
application sub category: topic_0769
application sub category: topic 3168
citation: btz808
citation: pmcid:PMC7703765
citation: pubmed:31697323
description: Building blocks for efficient handling of large Hi-C datasets. Framework for Storing and Accessing Hi-C Data Through HDF Files. HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization
feature list: operation_0337
license: MIT

HiCNAtra
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 2640
application sub category: topic 3169
application sub category: topic 3673
citation: https://doi.org/10.1101/798710
description: Identification and Utilization of Copy Number Information for Correcting Hi-C Contact Map of Cancer Cell Line. An analytical and visualization tool for CNV discovery and contact map correction of Hi-C/3C-seq data of cancer cell lines. HiCNAtra is a MATLAB-based tool that accepts HDF5 files, the output of hiclib after applying the iterative-mapping technique, as input. HiCNAtra pipeline is divided into three modules: 1) computation of the read depth (RD) signal from Hi-C or 3C-seq reads (RD calculator), 2) RD-based detection of copy number events based on CNAtra approach (CNV caller) and 3) bias correction of chromatin interaction matrix introduced by CNVs and other systematic biases (Contact map corrector)
feature list: operation_0392
feature list: operation 3435
feature list: operation 3659

HiCNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3474
citation: btz251
citation: pmcid:PMC6821373
citation: pubmed:31056636
description: Computational method for resolution enhancement of Hi-C data. It uses a very deep convolutional neural network to learn the mapping between low-resolution and high-resolution Hi-C contact matrices.
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: HiCNN package.tar.gz
primary contact: Zheng Wang

HiCeekR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0654
application sub category: topic 3169
application sub category: topic 3170
application sub category: topic 3295
application sub category: topic 3382
citation: FGENE.2019.01079
citation: pmcid:PMC6844183
citation: pubmed:31749839
description: A Novel Shiny App for Hi-C Data Analysis. R package that allows easily performing a complete Hi-C data analysis through a Graphical User Interface. HiCeekR is a novel Shiny based R package for Hi-C data analysis
feature list: operation_0337
feature list: operation 3435
feature list: operation 3695
feature list: operation 3798
license: GPL-2.0

HiLight-PTM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: btz654
citation: pmcid:PMC9883675
citation: pubmed:31424526
description: An Online Application to Aid Matching Peptide Pairs with Isotopically Labelled PTMs | MOTIVATION:Database searching of isotopically labelled PTMs can be problematic and we frequently find that only one, or neither in a heavy light pair are assigned. In such cases, having a pair of MS MS spectra that differ due to an isotopic label can assist in identifying the relevant m z values that support the correct peptide annotation or can be used for de novo sequencing. RESULTS:We have developed an online application that identifies matching peaks and peaks differing by the appropriate mass shift (difference between heavy and light PTM) between two MS MS spectra. Furthermore, the application predicts, from the exact-match peaks, the mass of their complementary ions and highlights these as high confidence matches between the two spectra
feature list: operation 3638
feature list: operation 3644
feature list: operation 3755

HiPFSTA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0593
application sub category: topic 3384
application sub category: topic 3385
citation: journal.pone.0207376
citation: pmcid:PMC6283589
citation: pubmed:30521560
description: Gradient-based, GPU-accelerated, high-precision contour-segmentation algorithm with application to cell membrane fluctuation spectroscopy.
feature list: operation 3629
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

HiPPO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0108
application sub category: topic 2229
application sub category: topic 2830
application sub category: topic 3489
citation: CMB.2019.0384
citation: pubmed:31855463
description: Two Bioinformatics Tools to Support Analysis of Mass Cytometry Data. High-dimensional mass cytometry (Cytometry by Time-Of-Flight; CyTOF) is a multiparametric single-cell approach that allows for more than 40 parameters to be evaluated simultaneously, opening the possibility to dissect cellular heterogeneity and elucidate functional interactions between different cell types. However, the complexity of these data makes analysis and interpretation daunting. We created High-throughput Population Profiler (HiPPO), a tool that reduces the complexity of the CyTOF data and allows homogeneous clusters of cells to be visualized in an intuitive manner. Each subpopulation is mapped to the Population Analysis Database (PANDA), an open-source, manually curated database containing protein expression profiles for selected markers of primary cells, allowing for cell type abundance in the analyzed samples to be monitored.
feature list: operation_0337
feature list: operation 2495
feature list: operation 3432

HighResNPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0769
application sub category: topic 2840
application sub category: topic 3520
citation: BKZ030
citation: pubmed:31095696
description: Online Crowd-Sourced HR-MS Database for Suspect and Non-targeted Screening of New Psychoactive Substances.
feature list: operation 2929
feature list: operation 3431
feature list: operation 3629
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Marie Mardal

Hintra
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic 3293
citation: BTZ355
citation: pmcid:PMC6612880
citation: pubmed:31510674
description: Collaborative intra-tumor heterogeneity detection | An algorithm for collaborative intra-tumor heterogeneity detection | We introduce a method called Hintra for intra-tumor heterogeneity detection | Despite the remarkable advances in sequencing and computational techniques, noise in the data and complexity of the underlying biological mechanisms render deconvolution of the phylogenetic relationships between cancer mutations difficult
feature list: operation_0567
feature list: operation 3478
feature list: operation 3629

HippMapp3r
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3360
application sub category: topic 3384
application sub category: topic 3474
citation: hbm.24811
citation: pmcid:PMC7267905
citation: pubmed:31609046
description: Hippocampal segmentation for brains with extensive atrophy using three-dimensional convolutional neural networks. Welcome to HippMapp3r’s documentation! — HippMapp3r documentation. Free document hosting provided by Read the Docs
feature list: operation 3435

HisgAtlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 2830
application sub category: topic 3360
application sub category: topic 3400
citation: bax094
citation: pmcid:PMC7243927
citation: pubmed:31725860
description: A human immunosuppression gene database. HisgAtlas is the first database that stores a list of immunosuppression genes collected by literature mining and manual curation. 995 human immunosuppression genes and 260 associated diseases are collected in this database. The user needs to log in for the curation. Please refer to our FAQ for detail. HisgAtlas is a manual curation database for human immunosuppression genes.
feature list: operation_0306
feature list: operation 2421
feature list: operation 2428
software help: Help

HistoneAnalysisWorkflow
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic 3295
application sub category: topic 3520
citation: J.YMETH.2019.12.001
citation: pubmed:31816396
description: A practical guide for analysis of histone post-translational modifications by mass spectrometry. Workflow to perform data quality checks, filtering, normalization, statistics, and visualization for histone PTM data run through EpiProfile 2.0. Workflow to perform data quality checks, filtering, normalization, statistics, and visualization for histone PTM data run through EpiProfile 2.0 or Skyline software. Raw data and example scripts can be found at: doi:10.25345/C5ZQ0F.
feature list: operation_0417
feature list: operation 3435
feature list: operation 3645

HmtVar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0218
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic_0769
application sub category: topic 2229
citation: mgg3.1085
citation: pmcid:PMC7005629
citation: pubmed:31821723
description: A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. The main web resource to explore human mitochondrial variability data and their pathological correlation. HmtVar is a manually-curated database offering variability and pathogenicity information about mtDNA variants. Data are gathered from HmtVar's twin database HmtDB, and further integrated with pathogenicity predictions as well as additional information from several online resources focused on mtDNA, such as MITOMAP, 1000 Genomes Project, MutPred, SNPs&GO and many others.
feature list: operation_0224
feature list: operation_0306
feature list: operation 3227
feature list: operation 3461
feature list: operation 3778

HogProf
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0621
application sub category: topic_0623
application sub category: topic 3293
application sub category: topic 3372
citation: https://doi.org/10.1101/852491
description: Scalable Phylogenetic Profiling using MinHash Uncovers Likely Eukaryotic Sexual Reproduction Genes. Phylogenetic profiling with orthology data. HogProf is an extensible and tunable approach to phylogenetic profiling using orthology data. It is powered by minhash based datastructures and computationally efficient
feature list: operation_0539
feature list: operation_0540
feature list: operation 3478
license: MIT

Holden
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
application sub category: topic 3379
application sub category: topic 3474
citation: https://doi.org/10.1101/757070
description: Detecting fabrication in large-scale molecular omics data | Fraud is a pervasive problem and can occur as fabrication, falsification, plagiarism or theft. The scientific community is not exempt from this universal problem and several studies have recently been caught manipulating or fabricating data. Current measures to prevent and deter scientific misconduct come in the form of the peer-review process and on-site clinical trial auditors. As recent advances in high-throughput omics technologies have moved biology into the realm of big-data, fraud detection methods must be updated for sophisticated computational fraud | In the financial sector, machine learning and digit-preference are successfully used to detect fraud | See our pre-press article at: https://www.biorxiv.org/content/10.1101/757070v1
feature list: operation 3557
feature list: operation 3891

Holmes
type: SoftwareApplication
input: Simulation
  type: FormalParameter
  additional type: data 3869
  encoding format: format 3983
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2259
citation: btx492
citation: pubmed:28961696
description: Graphical tool for development, simulation and analysis of Petri net based models of complex biological systems.
feature list: operation_0244
feature list: operation 2426
is accessible for free: true
license: Artistic-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: HolmesEN.pdf
primary contact: Piotr Formanowicz

Hotspot analysis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
citation: PEERJ.PREPRINTS.2204V2
citation: PEERJ.PREPRINTS.2204V3
citation: PEERJ.PREPRINTS.2204V4
description: A first prototype Python plugin enabling exploratory spatial data analysis into QGIS. A QGIS plugin for hotspot analyis. Hotspot Analysis Plugin for QGIS.
feature list: operation_0451
feature list: operation 3435

Housekeeping and Reference Transcript Atlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0632
application sub category: topic 3170
application sub category: topic 3307
application sub category: topic 3361
application sub category: topic 3512
application sub category: topic 3518
application sub category: topic 3678
citation: gkaa609
citation: pmcid:PMC7778946
citation: pubmed:32663312
description: Redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets. Web-based tools to search tissue specific housekeeping genes.
feature list: operation 2424
feature list: operation 3799
feature list: operation 3840
is accessible for free: true
software help: http://housekeeping.unicamp.br/
software version: 1.0

HowDe-SBT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
citation: btz662
citation: pmcid:PMC8215923
citation: pubmed:31504157
description: Improved representation of sequence Bloom trees | Sequence Bloom Tree, supporting determined/how split filters | Jellyfish (Version 2.2.0 or later)
feature list: operation_0224
license: MIT

HumCFS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0634
application sub category: topic_0654
application sub category: topic_0659
citation: s12864-018-5330-5
citation: pmcid:PMC7402404
citation: pubmed:30999860
description: Manually curated database of human chromosomal fragile sites. HumCFS provides useful information on fragile sites such as coordinates on the chromosome, cytoband, their chemical inducers and frequency of fragile site (rare or common), genes and miRNAs lying in fragile sites.
feature list: operation 3501
feature list: operation 3792
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Dr. Gajendra P. S. Raghava

HumanMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: HumanMine integrates many types of data for Homo sapiens and Mus musculus
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: index
software help: intermine-user-docs
software version: 6.0 2019 May

Hurdle
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 2269
citation: 18-AOAS1213
citation: pmcid:PMC6684253
citation: pubmed:31388390
description: Estimation and sampling for multi-dimensional Hurdle models on a Normal density with applications to single-cell co-expression | A Hurdle model is a modification of a distribution at zero. This package provides routines to estimate and sample from multivariate Hurdle models on a Normal density. These are distributions that are conditionally Normal, but with singularities along the coordinate axes, so generalize a univariate zero-inflated distribution
feature list: operation 3436
feature list: operation 3463
feature list: operation 3501

HyAsP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3315
application sub category: topic 3673
citation: btz413
citation: pubmed:31116364
description: HyAsP (Hybrid Assember for Plasmids) - tool that identifies, bins and assembles plasmid contigs following a hybrid approach based on a database of known plasmids genes and a greedy assembly algorithm.
feature list: operation_0578
feature list: operation 3482
feature list: operation 3798
is accessible for free: true
license: MIT
operating system: Linux
software help: README.md
primary contact: Cedric Chauve

HyPhy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0084
application sub category: topic_0154
application sub category: topic_0602
author: Art FY Poon
author: Sergei L Kosakovsky Pond
author: Steven Weaver
citation: 978-1-4939-8736-8 6
citation: bti079
citation: pubmed:15509596
citation: pubmed:30298394
description: Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.
feature list: operation 2238
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: hyphy
software help: tutorials

HybPiper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0194
application sub category: topic_0196
application sub category: topic_0780
application sub category: topic 3293
application sub category: topic 3512
citation: https://doi.org/10.1101/854232
description: Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae). Recovering genes from targeted sequence capture data. Current version: 1.3.1 (August 2018). -- Read our article in Applications in Plant Sciences (Open Access). HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.
feature list: operation_0310
feature list: operation 3192
feature list: operation 3198
license: GPL-3.0

HybridMolDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic_0209
citation: ACS.JCIM.9B00314
citation: pubmed:31524396
description: A Manually Curated Database Dedicated to Hybrid Molecules for Chemical Biology and Drug Discovery | Hybrid Molecules is defined as the design of new chemical molecule that hybridizes two or more pharmacophoric moieties from known identical or non-identical bioactive molecules, or two or more known identical or non-identical bioactive molecules directly into a single molecule to obtain better affinity and efficacy or to improve the properties of the parent molecules or to interact with two or multiple targets or to reduce undesirable side effects or to decrease in drug-drug interactions or reduce emergence of drug resistance | Hybrid Molecule Database (HybridMolDB) provides a versatile resource for the display, search, and analysis of the structure, manual-annotated design protocol, the pharmacological data, some physicochemical and ligand efficiency and druglike and ADMET characteristics and the proﬁle of targets of the well-known hybrid molecules
feature list: operation_0337
feature list: operation 3456
feature list: operation 3893

HydroSight
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic 2269
application sub category: topic 3382
citation: GWAT.12946
citation: pubmed:31569268
description: Joint Estimation of Gross Recharge, Groundwater Usage, and Hydraulic Properties within HydroSight. A toolbox for data-driven hydrogeological insights. Websites for you and your projects, hosted directly from your GitHub repository. Just edit, push, and your changes are live. Websites for you and your projects. HydroSight is a highly flexible statistical toolbox for quantitative hydrogeological insights. It comprises of a powerful groundwater hydrograph time-series modelling and simulation framework plus a data quality analysis module. Multiple models can be built for one bore, allowing statistical identification of the dominant processes, or 100’s of bores can be modelled to quantify aquifer heterogeneity. This flexibility allows many novel applications such as:.
feature list: operation 3096
feature list: operation 3431
feature list: operation 3799

HymenopteraMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: An integrated data warehouse for the Hymenoptera Genome Database
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 1.4

HypercubeME
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0625
citation: https://doi.org/10.1101/741827
description: Two hundred million combinatorially complete datasets from a single experiment | Generate all combinatorially complete datasets from the given genotype list | python3 HypercubeME.py -g test_complete_03.txt | Run in the command line following examples: | See the file 'test_complete_03.txt' for input example. Columns are tab-separated, first line is a header which is ignored by HypercubeME. First column (example: '0C:2T') is a column-separated mutation list of a particular mutant variant. Each mutation consists of mutated position and the variant (amino acid residue or RNA/DNA base) where it is mutated. For wild-type HypercubeME uses '0Z', where 'Z' means wild-type variant (amino acid residue or RNA/DNA base); however, in the genotype file wild-type can also be denoted as empty string as in the file 'test_complete_03.txt'. All other columns are ignored by HypercubeME
feature list: operation 3196
license: GPL-3.0

Hypergraph Dynamic Correlation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic 3170
application sub category: topic 3308
citation: S12864-019-5787-X
citation: pmcid:PMC6530038
citation: pubmed:31117943
description: Method to construct module-level three-way interaction networks. The method is able to present integrative uniform hypergraphs to reflect the global dynamic correlation pattern in the biological system, providing guidance to down-stream gene triplet-level analyses.
feature list: operation 3463
feature list: operation 3501
feature list: operation 3766
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0003-2502-1628

Hypocotyl
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 3382
application sub category: topic 3474
citation: pp.19.00728
citation: pubmed:31636105
description: A Deep Learning-Based Approach for High-Throughput Hypocotyl Phenotyping. A deep learning-based approach for high throughput plant phenotyping. This repository is the companion for the paper A deep learning-based approach for high throughput plant phenotyping, Dobos et al.. The dataset used in the article can be found at this page. Using a trained model for measuring hypocotyls. The pretrained model used in the research article can be downloaded here.
feature list: operation 3443
feature list: operation 3553
feature list: operation 3799

Hyppo-X
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0780
application sub category: topic 3298
application sub category: topic 3315
citation: TCBB.2019.2947500
citation: pubmed:31647442
description: A Scalable Exploratory Framework for Analyzing Complex Phenomics Data. A header only software library helps to visually discover the insights of high dimensional complex data set. We can represent the category of points in a cluster using a pie chart. In our Hyppo-X framework, we have capability to define a category of a point using single or multiple columns of the dataset. Pie chart shows the percentage distribution of points among all categories. For instance, for the above sample dataset, we can define the locaion column named Loc as the category of all the points then we will get following graphs. Here, blue color indicates points those belong in location N and red color indicates points those belong in location K. This graph with pie chart node helps us to understand the behavior of points with respect to two locations. This software library is built to delve the insights of a complex high dimensional dataset
feature list: operation_0282
feature list: operation_0337
feature list: operation 1812
feature list: operation 3432
feature list: operation 3891

I-Impute
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/772723
description: A self-consistent method to impute single cell RNA sequencing data | I-Impute is a “self-consistent” method method to impute scRNA-seq data. I-Impute leverages continuous similarities and dropout probabilities and refines the data iteratively to make the final output "self-consistent". I-Impute exhibits robust imputation ability and follows the “self-consistency” principle. It offers perspicacity to uncover the underlying cell subtypes in real scRNA-Seq data
feature list: operation 3557
feature list: operation 3891
license: MIT

I3
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic 3056
application sub category: topic 3574
citation: j.gpb.2018.10.006
citation: pmcid:PMC7056857
citation: pubmed:31765831
description: A Self-organising Learning Workflow for Intuitive Integrative Interpretation of Complex Genetic Data. Intuitive Integrative Interpretation (I3) of complex genetic data. 3 Interpreting genetics of gene expression in brains. 1 State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China

IA-Lab
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 3374
application sub category: topic 3382
citation: JOURNAL.PONE.0220627
citation: pmcid:PMC6675096
citation: pubmed:31369634
description: A MATLAB framework for efficient microscopy image analysis development, applied to quantifying intracellular transport of internalized peptide-drug conjugate | IA-Lab: a MATLAB-based framework for high throughput custom image analysis | This is the central repo for the IALab software, including parsers of various microscopy experiments, into multidimensional and multichannel images, and core code for segmentation, measurement, export of results and display of images and results . Some example workflows are stored in the Examples directory
feature list: operation_0337
feature list: operation 3436
feature list: operation 3443
license: LGPL-3.0

IAMBEE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic_0625
citation: GKZ451
citation: pmcid:PMC6602435
citation: pubmed:31127271
description: Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE) - web server designed for network-based genotype-phenotype mapping of clonal populations that display the same focal phenotype.
feature list: operation 3196
feature list: operation 3216
feature list: operation 3280
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial
primary contact: https://orcid.org/0000-0002-9998-2408

IBD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3305
application sub category: topic 3337
citation: https://doi.org/10.1101/749507
description: iLASH - IBD Estimation Using Locality Sensitive Hashing | iLASH: Ultra-Rapid Detection of IBD Tracts | iLASH divides the genotype data in consecutive slices and then runs LSH algorithm over each slice. Slices (windows) are, thus, the building blocks of IBD tracts. The following parameters control different properties of these slices
feature list: operation_0487
feature list: operation 3196
feature list: operation 3211

IBS-privacy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3056
application sub category: topic 3518
citation: https://doi.org/10.1101/798272
description: Attacks on genetic privacy via uploads to genealogical databases. Create figures for "Attacks on genetic privacy via uploads to genealogical databases" by Michael D. Edge and Graham Coop. README for gedmatch figures & emails. The files marked GEDmatch_*_Redacted.pdf are printouts of the display of the GEDmatch 1-to-1 match genome browser.
feature list: operation_0484
feature list: operation_0487
feature list: operation 3196
feature list: operation 3557

IBiSS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0611
application sub category: topic 2828
citation: btv347
citation: pubmed:26092861
description: Tool for integrated sequence and 3D structure analysis of large macromolecular complexes.
feature list: operation_0448
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Manual IBiSS V1.00.pdf
primary contact: Bruno P. Klaholz

ICA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2640
application sub category: topic 3172
application sub category: topic 3308
citation: IJMS20184414
citation: pmcid:PMC6771121
citation: pubmed:31500324
description: Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets | ICA-in-Cancer-research-review-materials | Jupyter Notebook containing example of Independent Component Analysis (ICA) accompanying the review in Internal Journal of Molecular Sciences (IJMS) | "Independent Component Analysis of BIg Omics Data" | BIODICA: Independent Component Analysis for BIg Omics Data | Deconvolution of transcriptome through Immune Component Analysis | BIODICA is a user-friendly pipline for high-performant computation of independent components for omics data, using stability analysis and computing the optimal number of the components from their stabilities, and performing analyses for interpreting the results of ICA application | You can install deconICA from GitHub with: | AN R PACKAGE FOR IDENTIFYING IMMUNE-RELATED SIGNALS IN TRANSCRIPTOME THROUGH DECONVOLUTION OR UNSUPERVISED SOURCE SEPARATION METHODS
feature list: operation 2939
feature list: operation 3629
feature list: operation 3891
license: GPL-2.0

ICCS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0593
application sub category: topic 3295
application sub category: topic 3306
application sub category: topic 3385
citation: J.BPJ.2019.10.036
citation: pmcid:PMC6895719
citation: pubmed:31732142
description: Nanoscale Distribution of Nuclear Sites by Super-Resolved Image Cross-Correlation Spectroscopy. User-fiendly code for image cross-correlation specroscopy (ICCS) analysis based on the following article:
feature list: operation 3435
feature list: operation 3443

ICGRM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3500
citation: S12859-019-3319-Y
citation: pmcid:PMC6933885
citation: pubmed:31878869
description: Integrative construction of genomic relationship matrix combining multiple genomic regions for big dataset. BACKGROUND:Genomic prediction is an advanced method for estimating genetic values, which has been widely accepted for genetic evaluation in animal and disease-risk prediction in human. It estimates genetic values with genome-wide distributed SNPs instead of pedigree. The key step of it is to construct genomic relationship matrix (GRM) via genome-wide SNPs; however, usually the calculation of GRM needs huge computer memory especially when the SNP number and sample size are big, so that sometimes it will become computationally prohibitive even for super computer clusters. We herein developed an integrative algorithm to compute GRM.
feature list: operation_0484
feature list: operation 3196
feature list: operation 3359

ICLabel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0749
application sub category: topic 3304
application sub category: topic 3474
citation: J.NEUROIMAGE.2019.05.026
citation: pmcid:PMC6592775
citation: pubmed:31103785
description: Automated electroencephalographic independent component classifier, dataset, and website.
feature list: operation 3629
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial
primary contact: Luca Pion-Tonachini

ICU readmissions
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3403
application sub category: topic 3474
citation: https://doi.org/10.1101/2019.12.26.19015909
description: Accurate and reproducible prediction of ICU readmissions. The code in this repository was used to produce the results of this paper (awaiting acceptance, link will be updated). A walkthrough can be found in this notebook.
license: GPL-3.0

IDADE2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic 3399
citation: AJPA.23856
citation: pubmed:31087665
description: Web server for adult age estimation of human skeletal remains.
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Allysha Winburn
primary contact: Carme Rissech Badallo
primary contact: Marta San-Millán

IDBac
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 1915
  encoding format: format 2333
  encoding format: format 3244
  encoding format: format 3245
  encoding format: format 3654
output: Data
  type: FormalParameter
  additional type: data_0006
  encoding format: format 3621
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Library
application sub category: topic_0121
application sub category: topic 3172
application sub category: topic 3301
application sub category: topic 3336
application sub category: topic 3697
author: http://orcid.org/0000-0001-6439-9397
citation: pnas.1801247115
citation: https://doi.org/10.3791/59219
citation: pmcid:PMC5949002
citation: pmcid:PMC7204650
citation: pubmed:29686101
citation: pubmed:31157770
description: A MALDI bioinformatics platform for analyzing protein and small molecule MALDI-TOF MS data (with a particular focus on mic organism analysis )
feature list: operation_0567
feature list: operation 2409
feature list: operation 2939
feature list: operation 3214
feature list: operation 3432
feature list: operation 3694
feature list: operation 3744
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.1.10

IDDomainSpotter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0593
application sub category: topic_0736
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3306
citation: PRO.3754
citation: pmcid:PMC6933863
citation: pubmed:31642121
description: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors. IDDomainSpotter – Section for Biomolecular Sciences. IDDomainSpotter is a sequence-based approach to assess and visualize domain organisation in long intrinsically disordered proteins based on compositional biases
feature list: operation_0303
feature list: operation_0337
feature list: operation 3904

IDH-wild-type
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0621
application sub category: topic 2269
application sub category: topic 3360
citation: VDZ007
citation: pmcid:PMC6777501
citation: pubmed:31608326
description: An independently validated nomogram for isocitrate dehydrogenase-wild-type glioblastoma patient survival. Background:In 2016, the World Health Organization reclassified the definition of glioblastoma (GBM), dividing these tumors into isocitrate dehydrogenase (IDH)-wild-type and IDH-mutant GBM, where the vast majority of GBMs are IDH-wild-type. Nomograms are useful tools for individualized estimation of survival. This study aimed to develop and independently validate a nomogram for IDH-wild-type patients with newly diagnosed GBM.
feature list: operation 2428
feature list: operation 3503
feature list: operation 3659

IDSM
type: SoftwareApplication
input: Query script
  type: FormalParameter
  additional type: data 3786
  encoding format: format 3790
output: Database search results
  type: FormalParameter
  additional type: data 2080
  encoding format: format 2331
  encoding format: format 2332
  encoding format: format 3255
  encoding format: format 3256
  encoding format: format 3261
  encoding format: format 3464
  encoding format: format 3475
  encoding format: format 3752
  encoding format: format 3956
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: SPARQL endpoint
additional type: Web application
additional type: Web service
application sub category: topic 2258
application sub category: topic 3343
application sub category: topic 3369
author: 0000-0002-7038-544X
author: https://orcid.org/0000-0001-7356-4075
citation: s13321-019-0367-2
citation: s13321-021-00515-1
citation: pmcid:PMC6599361
citation: pmcid:PMC8117646
citation: pubmed:31254167
citation: pubmed:33980298
description: Integrated Database of Small Molecules
feature list: operation 2421
is accessible for free: true
software help: manual.html
primary contact: 0000-0002-7038-544X

IDTxl
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3304
application sub category: topic 3384
citation: NETN A 00092
citation: pmcid:PMC6663300
citation: pubmed:31410382
description: Large-scale directed network inference with multivariate transfer entropy and hierarchical statistical testing | The Information Dynamics Toolkit xl (IDTxl) is a comprehensive software package for efficient inference of networks and their node dynamics from multivariate time series data using information theory. IDTxl provides functionality to estimate the following measures:
feature list: operation 3216
feature list: operation 3658
license: GPL-3.0

IILLS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3063
application sub category: topic 3324
citation: S12859-019-3278-3
citation: pmcid:PMC6933616
citation: pubmed:31881820
description: Predicting virus-receptor interactions based on similarity and semi-supervised learning. BACKGROUND:Viral infectious diseases are the serious threat for human health. The receptor-binding is the first step for the viral infection of hosts. To more effectively treat human viral infectious diseases, the hidden virus-receptor interactions must be discovered. However, current computational methods for predicting virus-receptor interactions are limited. RESULT:In this study, we propose a new computational method (IILLS) to predict virus-receptor interactions based on Initial Interaction scores method via the neighbors and the Laplacian regularized Least Square algorithm. IILLS integrates the known virus-receptor interactions and amino acid sequences of receptors. The similarity of viruses is calculated by the Gaussian Interaction Profile (GIP) kernel. On the other hand, we also compute the receptor GIP similarity and the receptor sequence similarity.
feature list: operation_0303

ILMF-VH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
application sub category: topic 3301
application sub category: topic 3837
citation: S12859-019-3082-0
citation: pmcid:PMC6886165
citation: pubmed:31787095
description: Predicting virus-host association by Kernelized logistic matrix factorization and similarity network fusion. Kernelized Logistic Matrix Factorization based on Similarity Network Fusion for Predicting Virus-host Association. Xingpeng Jiang, xpjiang@mail.ccnu.edu.cn Dan Liu, liudan@mails.ccnu.edu.cn.
feature list: operation 2422
feature list: operation 3435
feature list: operation 3439

ImmunoDataAnalyzer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0632
application sub category: topic_0769
application sub category: topic_0804
application sub category: topic 3168
application sub category: topic 3474
citation: S12859-021-04535-4
citation: pmcid:PMC8734366
citation: pubmed:34991455
description: The ImmunoDataAnalyzer (IMDA) pipeline provides various methods for analysing immunological next-generation sequencing (NGS) data.
feature list: operation_0337
feature list: operation 3192
feature list: operation 3200
feature list: operation 3933
is accessible for free: true
license: Freeware
operating system: Linux
operating system: Windows

IMG-ABC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3174
application sub category: topic 3297
application sub category: topic 3407
citation: gkz932
citation: pmcid:PMC7145673
citation: pubmed:31665416
description: An update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase. The public IMG/ABC site has limited features and tools.
feature list: operation 2454
feature list: operation 3216
feature list: operation 3432

IMGT-ONTOLOGY
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Ontology
application sub category: topic 3930
application sub category: topic 3948
citation: j.biochi.2007.09.003
citation: https://doi.org/10.1093/bioinformatics/15.12.1047
citation: https://doi.org/10.16966/2470-102
citation: mabs.3.1.14151
citation: pmcid:PMC3038005
citation: pubmed:10745995
citation: pubmed:15089751
citation: pubmed:17949886
citation: pubmed:21099347
citation: pubmed:22654892
description: IMGT-ONTOLOGY is the first ontology for immunogenetics and immunoinformatics. It provides a semantic specification of the terms to be used in immunogenetics and immunoinformatics and manages the related knowledge, thus allowing the standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. IMGT-ONTOLOGY manages the knowledge through diverse facets relying on seven axioms, "IDENTIFICATION", "CLASSIFICATION", "DESCRIPTION", "NUMEROTATION", "LOCALIZATION", "ORIENTATION" and "OBTENTION". These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized.
feature list: operation 3501
software help: ontology.php

IMGT 2Dstructure-DB
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2330
input: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
input: Ontology concept
  type: FormalParameter
  additional type: data 2858
  encoding format: format 2330
output: Sequence report
  type: FormalParameter
  additional type: data 2955
  encoding format: format 2331
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 3930
application sub category: topic 3948
citation: gku1056
citation: pmcid:PMC4383898
citation: pubmed:25378316
description: IMGT/2Dstructure-DB is the IMGT® database for 2D structures (IMGT Colliers de Perles) of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins and related proteins of the immune system (RPI). Annotation is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
feature list: operation_0564
feature list: operation 2416
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: IMGT3DstructureDBHelp.shtml

IMGT Allele-Align
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 2330
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0804
citation: gku1056
citation: pmcid:PMC4383898
citation: pubmed:15089751
citation: pubmed:15972004
citation: pubmed:25378316
description: IMGT/Allele-Align is the IMGT® tool for the comparison of two alleles highlighting the nucleotide and amino acid differences.
feature list: operation 2409
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

IMGT CloneSearch
type: SoftwareApplication
output: Map
  type: FormalParameter
  additional type: data 1274
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0804
citation: gku1056
citation: pmcid:PMC4383898
citation: pubmed:15089751
citation: pubmed:15972004
citation: pubmed:25378316
description: IMGT/CloneSearch is the IMGT® tool allowing the search of a clone in IMGT/LocusView. Search is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: IMGT/CloneSearch

IMGT Collier-de-Perles
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 2330
output: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0804
citation: pubmed:11862387
citation: pubmed:18208865
citation: pubmed:21632776
citation: pubmed:25378316
description: IMGT/Collier-de-Perles is the IMGT® tool to draw standardized IMGT 2D graphical representations, or IMGT Colliers de Perles, of variable (V), constant (C), groove (G) domains, starting from the user own domain amino acid sequences. IMGT Colliers de Perles are based on amino acid sequences gapped according to the IMGT-ONTOLOGY concept of IMGT unique numbering.
feature list: operation 2409
feature list: operation 2945
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: IMGTCollier-de-Perles.shtml

IMGT DomainDisplay
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
input: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
output: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0804
application sub category: topic 3510
application sub category: topic 3930
application sub category: topic 3948
citation: gku1056
citation: pmcid:PMC4383898
citation: pubmed:25378316
description: IMGT/DomainDisplay is the IMGT® tool for the display of the amino acid sequences of the variable (V), constant (C) and groove (G) domains. Analysis is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: IMGTDomainGapAlign.shtml

IMGT DomainGapAlign
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
output: Protein alignment
  type: FormalParameter
  additional type: data 3154
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0804
application sub category: topic 3930
application sub category: topic 3948
citation: gkp946
citation: gku1056
citation: pdb.prot5636
citation: pmcid:PMC2808948
citation: pmcid:PMC4383898
citation: pubmed:19900967
citation: pubmed:21632775
citation: pubmed:25378316
description: IMGT/DomainGapAlign is the IMGT® tool for the analysis of amino acid sequences of variable (V), constant (C) or groove (G) domains. Analysis is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0491
feature list: operation 2479
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: IMGTDomainGapAlign.shtml

IMGT DomainSuperimpose
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0081
citation: gku1056
citation: pmcid:PMC4383898
citation: pubmed:25378316
description: IMGT/DomainSuperimpose is the IMGT® tool to superimpose 3D structures of two domains from IMGT/3Dstructure-DB. Domain 3D structures are numbered according to the IMGT-ONTOLOGY concept of IMGT unique numbering.
feature list: operation_0224
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: IMGTDomainSuperimpose.shtml

IMGT GENE-DB
type: SoftwareApplication
input: Ontology concept
  type: FormalParameter
  additional type: data 2858
  encoding format: format 2330
input: Gene name
  type: FormalParameter
  additional type: data 2299
  encoding format: format 2330
input: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2330
output: Sequence
  type: FormalParameter
  additional type: data 2044
  encoding format: format 1929
output: Database search results
  type: FormalParameter
  additional type: data 2080
  encoding format: format 2330
  encoding format: format 2331
output: Gene report
  type: FormalParameter
  additional type: data_0916
  encoding format: format 2330
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0804
application sub category: topic 3930
application sub category: topic 3948
citation: gki010
citation: gku1056
citation: pmcid:PMC4383898
citation: pmcid:PMC539964
citation: pubmed:15608191
citation: pubmed:25378316
description: IMGT/GENE-DB is the IMGT® database for immunoglobulin (IG) and T cell receptor (TR) genes and alleles (international nomenclature). Annotation is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
feature list: operation 2421
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: dataupdates.html
software help: programversions.html
software help: doc

IMGT GeneFrequency
type: SoftwareApplication
input: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2331
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2058
output: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0804
application sub category: topic 3053
application sub category: topic 3930
application sub category: topic 3948
citation: gku1056
citation: https://doi.org/10.1186/1471-2105-7-224
citation: pmcid:PMC1482724
citation: pmcid:PMC4383898
citation: pubmed:15972004
citation: pubmed:16640788
citation: pubmed:25378316
description: IMGT/GeneFrequency is the IMGT® tool providing the frequency usage of immunoglobulin (IG) and T cell receptor (TR) variable (V), diversity (D) and joining (J) genes in Homo sapiens and Mus musculus rearranged sequences from IMGT/LIGM-DB. Analysis is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation

IMGT GeneInfo
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2331
output: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 2331
output: Genetic map
  type: FormalParameter
  additional type: data 1278
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3930
application sub category: topic 3948
citation: gkh041
citation: gku1056
citation: https://doi.org/10.1186/1471-2105-7-224
citation: pmcid:PMC1482724
citation: pmcid:PMC308775
citation: pmcid:PMC4383898
citation: pubmed:14681357
citation: pubmed:16640788
citation: pubmed:25378316
description: IMGT/GeneInfo is the IMGT® tool providing combination (V-J and V-V) information for the human and mouse T cell receptor (TR) loci. Analysis is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
software help: Documentation.html

IMGT GeneSearch
type: SoftwareApplication
output: Map
  type: FormalParameter
  additional type: data 1274
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0804
application sub category: topic 3930
application sub category: topic 3948
citation: gku1056
citation: pmcid:PMC4383898
citation: pubmed:15089751
citation: pubmed:15972004
citation: pubmed:25378316
description: IMGT/GeneSearch is the IMGT® tool allowing the search of a gene in IMGT/LocusView. Search is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: IMGT/CloneSearch

IMGT GeneView
type: SoftwareApplication
output: Map
  type: FormalParameter
  additional type: data 1274
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0804
application sub category: topic 3930
application sub category: topic 3948
citation: gku1056
citation: pmcid:PMC4383898
citation: pubmed:15089751
citation: pubmed:15972004
citation: pubmed:25378316
description: IMGT® tool providing the view of a gene in IMGT/LocusView. Display is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: docs

IMGT HighV-QUEST
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 1929
output: Annotated text
  type: FormalParameter
  additional type: data 3779
  encoding format: format 3752
output: Sequence report
  type: FormalParameter
  additional type: data 2955
  encoding format: format 3752
output: Sequence features
  type: FormalParameter
  additional type: data 1255
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
additional type: Web application
application sub category: topic 3930
application sub category: topic 3948
citation: 978-1-61779-842-9 32
citation: gku1056
citation: https://doi.org/10.16966/2470-1025.103
citation: pmcid:PMC4383898
citation: pubmed:22665256
citation: pubmed:25378316
description: IMGT/HighV-QUEST is the IMGT® portal for NGS high-throughput nucleotide sequence analysis of immunoglobulins (IG) and T cell receptors (TR) variable domains, integrates IMGT/JunctionAnalysis and IMGT/Automat. Analysis is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0292
feature list: operation_0448
feature list: operation 2478
feature list: operation 3192
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: doc.action
software help: versions.action

IMGT JunctionAnalysis
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 2200
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
  encoding format: format 2331
output: Sequence alignment report
  type: FormalParameter
  additional type: data_0867
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3930
application sub category: topic 3948
citation: bth945
citation: gku1056
citation: pdb.prot5634
citation: pmcid:PMC4383898
citation: pubmed:15262823
citation: pubmed:21632777
citation: pubmed:25378316
description: IMGT/JunctionAnalysis is the IMGT® tool for the analysis of the nucleotide sequences of the V-J and V-D-J junctions of the variable domains of the immunoglobulins (IG) or antibodies and T cell receptors (TR). Analysis is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0292
feature list: operation_0448
feature list: operation 2478
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: user guide

IMGT LIGM-DB
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2330
input: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
input: EMBL/GenBank/DDBJ ID
  type: FormalParameter
  additional type: data 1103
  encoding format: format 2330
input: Ontology concept
  type: FormalParameter
  additional type: data 2858
  encoding format: format 2330
output: Database search results
  type: FormalParameter
  additional type: data 2080
  encoding format: format 1929
  encoding format: format 2330
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0080
application sub category: topic_0160
application sub category: topic_0804
application sub category: topic 3930
application sub category: topic 3948
citation: gkj088
citation: gku1056
citation: pmcid:PMC1347451
citation: pmcid:PMC4383898
citation: pubmed:16381979
citation: pubmed:25378316
description: IMGT/LIGM-DB is the IMGT® database for nucleotide sequences with translation of immunoglobulins (IG) and T cell receptors (TR). Annotation is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
feature list: operation_0338
feature list: operation_0361
feature list: operation_0564
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation

IMGT LocusView
type: SoftwareApplication
output: Sequence image
  type: FormalParameter
  additional type: data 2969
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0804
citation: scitranslmed.3009986
citation: pmcid:PMC5018401
citation: pubmed:15089751
citation: pubmed:15972004
citation: pubmed:25972004
description: IMGT/LocusView is the IMGT® tool providing a view of immunoglobulin (IG), T cell receptor (TR) and major histocompatibility (MH) loci. Display is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: docs

IMGT PRIMER-DB
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 2331
output: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 3930
application sub category: topic 3948
citation: gku1056
citation: pmcid:PMC4383898
citation: pubmed:15089751
citation: pubmed:15972004
citation: pubmed:25378316
description: IMGT/PRIMER-DB is the IMGT® database for oligonucleotides (primers) of immunoglobulins (IG) and T cell receptors (TR). Annotation is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
feature list: operation_0361
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: PrimerDB Help.pl

IMGT PhyloGene
type: SoftwareApplication
input: Ontology concept
  type: FormalParameter
  additional type: data 2858
  encoding format: format 2330
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2330
input: Gene name
  type: FormalParameter
  additional type: data 2299
  encoding format: format 2330
output: Sequence alignment report
  type: FormalParameter
  additional type: data_0867
  encoding format: format 1929
  encoding format: format 2331
output: Phylogenetic data
  type: FormalParameter
  additional type: data 2523
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3930
application sub category: topic 3948
citation: s0145-305x(03)00078-8
citation: gku1056
citation: pmcid:PMC4383898
citation: pubmed:12818634
citation: pubmed:25378316
description: IMGT/PhyloGene is the IMGT® tool to compute and draw phylogenetic trees for immunoglobulin (IG) and T cell receptor (TR) V-REGION nucleotide sequences. Analysis is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0292
feature list: operation_0499
is accessible for free: true
software help: IMGTPhylogenyDoc.html

IMGT StatClonotype
type: SoftwareApplication
input: Sequence report
  type: FormalParameter
  additional type: data 2955
  encoding format: format 3752
output: Plot
  type: FormalParameter
  additional type: data 2884
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2331
output: Heat map
  type: FormalParameter
  additional type: data 1636
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3930
application sub category: topic 3948
author: Safa Aouinti
citation: journal.pone.0142353
citation: journal.pone.0146702
citation: pmcid:PMC4634997
citation: pmcid:PMC4711580
citation: pubmed:26540440
citation: pubmed:26731095
description: IMGT/StatClnotype is the IMGT® tool for statistical analysis of sets from IMGT/HighV-QUEST output. IMGT/StatClonotype uses a generic statistical procedure for identifying significant changes in IG and TR differences of proportions of IMGT clonotypes (AA) diversity and expression. It uses the IMGT gene and allele nomenclature and it is based on IMGT-ONTOLOGY concepts.
feature list: operation_0315
feature list: operation 2238
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: IMGTStatClonotypeDoc.html
software help: upgrade

IMGT StructuralQuery
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2330
output: Structure
  type: FormalParameter
  additional type: data_0883
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0081
application sub category: topic_0804
citation: gkh042
citation: gku1056
citation: pmcid:PMC308776
citation: pmcid:PMC4383898
citation: pubmed:14681396
citation: pubmed:15089751
citation: pubmed:25378316
description: IMGT/StructuralQuery is the IMGT® tool to retrieve IMGT/3Dstructure-DB entries using amino acid structural criteria for variable (V), constant (C) or groove (G) domains. Annotation is based on the IMGT-ONTOLOGY concepts.
feature list: operation_0224
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: IMGT3DstructureDBHelp.shtml

IMGT mAb-DB
type: SoftwareApplication
input: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
output: Database search results
  type: FormalParameter
  additional type: data 2080
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0804
application sub category: topic 3400
application sub category: topic 3930
application sub category: topic 3948
citation: gku1056
citation: pmcid:PMC4383898
citation: pubmed:25378316
description: IMGT/mAb-DB is the IMGT® database for monoclonal antibodies (mAb) or immunoglobulins (IG), fusion proteins for immune applications (FPIA) and composite proteins for clinical applications (CPCA). IMGT/mAb-DB provides links to IMGT/2Dstructure-DB and IMGT/3Dstructure-DB.
feature list: operation_0224
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: doc
software help: upgrade program

IMMUNOPHARMACOLOGY
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic_0804
application sub category: topic 3172
application sub category: topic 3302
citation: gkz951
citation: pmcid:PMC7145572
citation: pubmed:31691834
description: Extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. IUPHAR Guide to IMMUNOPHARMACOLOGY. The IUPHAR/BPS Guide to IMMUNOPHARMACOLOGY. Description.
feature list: operation_0224
feature list: operation_0252

IMOS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0769
application sub category: topic 3794
citation: s12859-018-2592-5
citation: pmcid:PMC6345043
citation: pubmed:30678641
description: Aligner for mapping noisy long reads to the reference genome.
feature list: operation_0337
feature list: operation_0495
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Hadadian Nejad Youesfi

IMTRBM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3518
citation: JBHI.2018.2814609
citation: pubmed:29993787
description: Inferring MiRNA Targets based on Restricted Boltzmann Machines (IMTRBM) for prediction of miRNA-target interactions (MTIs).
feature list: operation_0463
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Y. Liu

INDEED
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0121
application sub category: topic 3172
application sub category: topic 3360
author: Zhenzhi Li
citation: BIBM.2018.8621426
citation: pmcid:PMC6549230
citation: pubmed:31179159
description: R package for network based differential expression analysis.
feature list: operation 3463
feature list: operation 3741
feature list: operation 3766
is accessible for free: true
license: Artistic-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Introduction to INDEED.html
software version: 1.2.0
primary contact: Yiming Zuo
primary contact: Zhenzhi Li

INDRA-IPM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic_0218
application sub category: topic_0602
citation: btz289
citation: pmcid:PMC6821420
citation: pubmed:31070726
description: Interactive pathway modeling using natural language with automated assembly.
feature list: operation_0533
feature list: operation 3083
is accessible for free: true
license: BSD-2-Clause
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Peter Sorger

INLA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic 2269
application sub category: topic 3810
citation: S00122-019-03424-Y
citation: pmcid:PMC6820601
citation: pubmed:31535162
description: Flexible modelling of spatial variation in agricultural field trials with the R package INLA | This is the site for the INLA approach to Bayesian inference within the R project for Statistical Computing | "Bayesian inference with INLA" by Virgilio Gómez-Rubio Another book from Virgilio is soon here. While we're waiting for the printed one, the current version is available as a github book; see the book section. May be ..
feature list: operation 2426
feature list: operation 3196
feature list: operation 3557

INSP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0218
application sub category: topic 3474
citation: J.AB.2019.113565
citation: pubmed:31883904
description: Discovering nuclear targeting signal sequence through protein language learning and multivariate analysis. Nuclear localization signals (NLSs) are peptides that target proteins to the nucleus by binding to carrier proteins in the cytoplasm that transport their cargo across the nuclear membrane. Accurate identification of NLSs can help elucidate the functions of nuclear protein complexes. The currently known NLS predictors are usually specific to certain species or largely dependent on prior knowledge of NLS basic residues. Thus, a more general predictor is highly desired to reduce the potentially high false positives or false negatives in discovering new NLSs. Here, we report a new method, INSP (Identification Nucleus Signal Peptide), to effectively identify NLS mainly based on statistical knowledge and machine learning algorithms.
feature list: operation_0418
feature list: operation 3631
feature list: operation 3767

INTERPRET DSS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0593
application sub category: topic 3384
application sub category: topic 3444
citation: https://doi.org/10.1186/1471-2105-11-581
citation: pmcid:PMC3004884
citation: pubmed:21114820
description: Software generated to aid in MRS analysis to achieve a specific diagnosis for brain lesions.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: How to evaluate a case with the INTERPRET DSS.pdf
software version: 3.2
primary contact: Biomedical Applications of Magnetic Resonance research group

IPA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3172
application sub category: topic 3520
citation: ACS.ANALCHEM.9B02354
citation: pubmed:31509381
description: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships | Integrated Probabilistic Annotation (IPA) - A Bayesian annotation method for LC/MS data integrating biochemical relations, isotope patterns and adduct formation
feature list: operation 3803

IPCAPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3056
citation: s13029-019-0072-6
citation: pmcid:PMC6427891
citation: pubmed:30936940
description: R package for iterative pruning to capture population structure.
feature list: operation_0484
feature list: operation_0487
feature list: operation 3196
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ipcaps
software version: 1.1.5
primary contact: Kridsadakorn Chaichoompu

IPD project
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0089
application sub category: topic_0199
application sub category: topic_0621
application sub category: topic 2830
application sub category: topic 3489
citation: S00251-019-01133-W
citation: pubmed:31641782
description: A centralised resource for the study of polymorphism in genes of the immune system. The Immuno Polymorphism Database. IPD was developed in 2003 to provide a centralised system for the study of polymorphism in genes of the immune system. The IPD project was established by the HLA Informatics Group of the Anthony Nolan Research Institute in close collaboration with the European Bioinformatics Institute.
feature list: operation_0416
feature list: operation 3197
feature list: operation 3431

IPEV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
description: Software tool to identify prokaryotic and eukaryotic virus-derived sequences in virome using deep learning. Used to calculate a set of scores that reflect the probability that input sequence fragments are prokaryotic and eukaryotic viral sequences.
feature list: operation 3460
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software version: V4

IPF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2229
application sub category: topic 3308
application sub category: topic 3322
citation: https://doi.org/10.1101/759902
description: Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis | Abstract We provide a single cell atlas of Idiopathic Pulmonary Fibrosis (IPF), a fatal interstitial lung disease, focusing on resident lung cell populations. By profiling 312,928 cells from 32 IPF, 29 healthy control and 18 chronic obstructive pulmonary disease (COPD) lungs, we demonstrate that IPF is characterized by changes in discrete subpopulations of cells in the three major parenchymal compartments: the epithelium, endothelium and stroma. Among epithelial cells, we identify a novel population of IPF enriched aberrant basaloid cells that co-express basal epithelial markers, mesenchymal markers, senescence markers, developmental transcription factors and are located at the edge of myofibroblast foci in the IPF lung
feature list: operation 3501
feature list: operation 3629

IRESpy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0108
application sub category: topic 3474
application sub category: topic 3512
citation: S12859-019-2999-7
citation: pmcid:PMC6664791
citation: pubmed:31362694
description: An XGBoost model for prediction of internal ribosome entry sites | BACKGROUND:Internal ribosome entry sites (IRES) are segments of mRNA found in untranslated regions that can recruit the ribosome and initiate translation independently of the 5' cap-dependent translation initiation mechanism. IRES usually function when 5' cap-dependent translation initiation has been blocked or repressed. They have been widely found to play important roles in viral infections and cellular processes. However, a limited number of confirmed IRES have been reported due to the requirement for highly labor intensive, slow, and low efficiency laboratory experiments. Bioinformatics tools have been developed, but there is no reliable online tool. RESULTS:This paper systematically examines the features that can distinguish IRES from non-IRES sequences
feature list: operation_0267
feature list: operation_0278
feature list: operation 3472

IRNdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic_0804
application sub category: topic 3512
citation: BAW138
citation: pmcid:PMC5091335
citation: pubmed:31414702
description: the database of immunologically relevant non-coding RNAs | git clone git@github.com:sschmeier/irndb2.git irndb2 | IRNdb - Database of immunologically relevant non-coding RNAs | // © Massey University 2014-2018 // v1.5.8
feature list: operation_0463
feature list: operation 2495
feature list: operation 3501

ISETBIO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic 2259
application sub category: topic 3382
application sub category: topic 3417
citation: JOURNAL.PCBI.1007063
citation: pmcid:PMC6553792
citation: pubmed:31125331
description: Image System Engineering Toolbox for Biology (ISETBIO) is a Matlab toolbox designed for calculating the properties of the front end of biological visual systems.
feature list: operation 3799
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: wiki
primary contact: https://orcid.org/0000-0002-4972-5307

ISEtools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 2269
application sub category: topic 3077
application sub category: topic 3372
citation: S19204544
citation: pmcid:PMC6832938
citation: pubmed:31635039
description: Semi-Automated Data Analysis for Ion-Selective Electrodes and Arrays Using the R Package ISEtools. Tools for Ion Selective Electrodes. Characterisation and calibration of single or multiple Ion Selective Electrodes (ISEs); activity estimation of experimental samples. Implements methods described in: Dillingham, P.W., Radu, T., Diamond, D., Radu, A. and McGraw, C.M. (2012) <doi:10.1002/elan.201100510> and Dillingham, P.W., Alsaedi, B.S.O. and McGraw, C.M. (2017) <doi:10.1109/ICSENS.2017.8233898>
feature list: operation_0337
feature list: operation 3435
feature list: operation 3659
license: GPL-2.0

ISIMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic 2229
application sub category: topic 3382
application sub category: topic 3474
citation: https://doi.org/10.1080/15376516.2019.1695303
citation: pubmed:31736404
description: Hep G2 cell culture confluence measurement in phase-contrast micrographs. Phase-contrast micrographs are often used for confirmation of proliferation and viability assays. However, they are usually only a qualitative tool and fail to exclude with certainty the presence of assay interference by test substances. The complexity of image analysis workflows hinders life scientists from routinely utilizing micrograph data. Here, we present an open-source software-based, combined ilastik segmentation ImageJ measurement of area (ISIMA) approach for cell monolayer segmentation and confluence percentage measurement of phase-contrast micrographs of Hep G2 cells. The aim of this study is to test whether the proposed approach is suitable for quantitative confirmation of proliferation data, acquired by the 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay.
feature list: operation 3443
feature list: operation 3799

ISeeU
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2269
application sub category: topic 3403
application sub category: topic 3474
citation: J.JBI.2019.103269
citation: pubmed:31430550
description: Visually interpretable deep learning for mortality prediction inside the ICU | To improve the performance of Intensive Care Units (ICUs), the field of bio-statistics has developed scores which try to predict the likelihood of negative outcomes. These help evaluate the effectiveness of treatments and clinical practice, and also help to identify patients with unexpected outcomes. However, they have been shown by several studies to offer sub-optimal performance. Alternatively, Deep Learning offers state of the art capabilities in certain prediction tasks and research suggests deep neural networks are able to outperform traditional techniques. Nevertheless, a main impediment for the adoption of Deep Learning in healthcare is its reduced interpretability, for in this field it is crucial to gain insight into the why of predictions, to assure that models are actually learning relevant features instead of spurious correlations
feature list: operation 3557
feature list: operation 3891
license: MIT

IWEPoissonPaper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0749
application sub category: topic 3295
citation: https://doi.org/10.1101/638023
description: Modeling methylation dynamics with simultaneous changes in CpG islands.
feature list: operation_0417
feature list: operation_0430
feature list: operation 3186
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Dirk Metzler

IgM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic_0632
application sub category: topic_0804
application sub category: topic 3360
citation: FIMMU.2019.02796
citation: pmcid:PMC6901697
citation: pubmed:31849974
description: Diagnostic Profiling of the Human Public IgM Repertoire With Scalable Mimotope Libraries. GENERATING AND TESTING MIMOTOPE LIBRARIES. Proof of pricniple diagnostic use with feature selection and predictor construction. comparison between IgM reactivity with different peptide libraries.
feature list: operation_0291
feature list: operation 2421
feature list: operation 2495

Illustrate
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0081
application sub category: topic 3382
application sub category: topic 3892
citation: J.STR.2019.08.011
citation: pmcid:PMC6834899
citation: pubmed:31519398
description: Software for Biomolecular Illustration | The small program Illustrate generates non-photorealistic images of biological molecules for use in dissemination, outreach, and education. The method has been used as part of the "Molecule of the Month," an ongoing educational column at the RCSB Protein Data Bank (http: rcsb.org). Insights from 20 years of application of the program are presented, and the program has been released both as open-source Fortran at GitHub and through an interactive web-based interface
feature list: operation_0337

ImJoy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3303
application sub category: topic 3382
application sub category: topic 3474
citation: S41592-019-0627-0
citation: pubmed:31780825
description: An open-source computational platform for the deep learning era. ImJoy -- Deep Learning Made Easy!
feature list: operation 3443
feature list: operation 3553
software help: docs

ImPLoc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0140
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3382
citation: BTZ909
citation: pubmed:31804670
description: A multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images. A deep learning model for protein subcellular localization based on immunohistochemistry images
feature list: operation_0418
feature list: operation_0477
feature list: operation 2489
feature list: operation 3436
feature list: operation 3552

ImSpectR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2830
application sub category: topic 3170
application sub category: topic 3400
citation: btz804
citation: pmcid:PMC7703782
citation: pubmed:31665245
description: R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data. R package to quantify CDR3 data for immune repertoire diversity. Author and Maintainer: Martijn Cordes. devtools::install_github("martijn-cordes/ImSpectR"). We also used ImSpectR to score CDR3 data from human TCR sequencing data sequenced with the ImmunoSeq platform. The CDR3 data scored by ImSpectR was data from CMV+ PBMCs published by Suessmuth et al. (Blood, 2015). Tab seperated (tsv) files were dowloaded from the Adaptive Biotech database for immunoSEQ data: https://clients.adaptivebiotech.com/pub/b4ac7a84-1e69-4d60-8254-845720454d7d
feature list: operation_0337
feature list: operation 3435
feature list: operation 3799

ImaGEO
type: SoftwareApplication
input: GEO accession number
  type: FormalParameter
  additional type: data 1147
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 1964
  encoding format: format 3475
  encoding format: format 3752
output: Heat map
  type: FormalParameter
  additional type: data 1636
output: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0091
application sub category: topic 3308
author: https://orcid.org/0000-0002-5186-0735
citation: bty721
citation: pubmed:30137226
description: ImaGEO is a web tool for gene expression Meta-Analysis that implements a complete and comprehensive meta-analysis workflow starting from Gene Expression Omnibus (GEO) dataset identifiers. The application integrates GEO datasets, applies different meta-analysis techniques and provides functional analysis results in an easy-to-use environment. ImaGEO is a powerful and useful resource that allows researchers to integrate and perform meta-analysis of GEO datasets to lead robust findings for biomarker discovery studies.
feature list: operation_0531
feature list: operation 3223
feature list: operation 3435
feature list: operation 3436
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-6173-7255

ImaGene
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3056
application sub category: topic 3474
citation: S12859-019-2927-X
citation: pmcid:PMC6873651
citation: pubmed:31757205
description: A convolutional neural network to quantify natural selection from genomic data. ImaGene implements a supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Specifically, it uses a convolutional neural network (CNN) which takes as input haplotypes for a population and locus of interest. It outputs confusion matrices as well as point estimates of the selection coefficient along with its posterior distribution and various metrics of confidence
feature list: operation 3196
feature list: operation 3799
feature list: operation 3802
license: GPL-3.0

ImageDataExtractor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0154
application sub category: topic 3068
application sub category: topic 3314
application sub category: topic 3382
application sub category: topic 3474
citation: ACS.JCIM.9B00734
citation: pubmed:31714792
description: A Tool To Extract and Quantify Data from Microscopy Images. Extract relevant images using ChemDataExtractor. Identify regions corresponding to individual particles
feature list: operation_0306
feature list: operation 3458
feature list: operation 3799
license: MIT

Imager-4D
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3444
application sub category: topic 3452
citation: s10278-019-00255-7
citation: pmcid:PMC6841823
citation: pubmed:31388864
description: New Software for Viewing Dynamic PET Scans and Extracting Radiomic Parameters from PET Data | Extensive research is currently being conducted into dynamic positron emission tomography (PET) acquisitions (including dynamic whole-body imaging) as well as extraction of radiomic features from imaging modalities. We describe a new PET viewing software known as Imager-4D that provides a facile means of viewing and analyzing dynamic PET data and obtaining associated quantitative metrics including radiomic parameters. The Imager-4D was programmed in the Java language utilizing the FX extensions. It is executable on any system for which a Java w FX compliant virtual machine is available. The software incorporates the ability to view and analyze dynamic data acquired with different types of dynamic protocols. For image display, the program maintains a built-in library of 62 different lookup tables with monochromatic and full-color distributions

ImaginR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 3382
application sub category: topic 3500
citation: S41598-019-43777-4
citation: pmcid:PMC6525208
citation: pubmed:31101851
description: Characterization of inner shell colour variations in Pinctada margaritifera assessed by HSV colour quantification.
feature list: operation 3799
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ImaginR.pdf
primary contact: Chin-Long Ky

ImmClass2019
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3400
citation: https://doi.org/10.1101/623082
description: An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets.
feature list: operation 2436
feature list: operation 3557
feature list: operation 3659
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: David J. Klinke

ImmPort
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0804
citation: sdata.2018.15
citation: pmcid:PMC5827693
citation: pubmed:29485622
description: Data repository with analysis tools that is mainly focused on cytometry and immunology.
feature list: operation_0224
feature list: operation 3431
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation
software help: tutorials

Immcantation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic 2830
application sub category: topic 3168
citation: https://doi.org/10.1101/788620
description: Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. Welcome to the Immcantation Portal! — Immcantation documentation. Free document hosting provided by Read the Docs
feature list: operation 3432
feature list: operation 3625
license: CC-BY-SA-4.0

ImmuCellAI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0804
application sub category: topic 2269
application sub category: topic 2640
application sub category: topic 3070
application sub category: topic 3400
citation: https://doi.org/10.1101/872184
description: A unique method for comprehensive T-cell subsets abundance prediction and its application in cancer immunotherapy. Copyright © Guo Lab , College of Life Science and Technology , HUST , China. Any comments and suggestions, please contact us
feature list: operation 2495
feature list: operation 3659

ImmuneRegulation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic_0749
application sub category: topic 3517
citation: GKZ450
citation: pmcid:PMC6602512
citation: pubmed:31114925
description: Web-based tool for identifying human immune regulatory elements.
feature list: operation_0441
feature list: operation 3196
feature list: operation 3232
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: faq.html
software help: tutorials.html
primary contact: https://orcid.org/0000-0002-7364-2202

ImmuneScape
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2275
application sub category: topic 2830
citation: 978-1-4939-9728-2 17
citation: pubmed:31396940
description: Structural Modeling of Lymphocyte Receptors and Their Antigens
feature list: operation_0416
feature list: operation_0477
feature list: operation_0478

ImmunomeBrowser
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0154
application sub category: topic 2830
citation: bty463
description: Tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins.
feature list: operation_0252
feature list: operation_0416
feature list: operation 3436
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: Sandeep Kumar Dhanda

ImpRes
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0089
application sub category: topic 3376
application sub category: topic 3419
citation: S13012-019-0897-Z
citation: pmcid:PMC6693182
citation: pubmed:31412887
description: Development, application, feasibility and preliminary evaluation of the implementation science research development (ImpRes) tool and guide | BACKGROUND:Designing implementation research can be a complex and daunting task, especially for applied health researchers who have not received specialist training in implementation science. We developed the Implementation Science Research Development (ImpRes) tool and supplementary guide to address this challenge and provide researchers with a systematic approach to designing implementation research. METHODS:A multi-method and multi-stage approach was employed. An international, multidisciplinary expert panel engaged in an iterative brainstorming and consensus-building process to generate core domains of the ImpRes tool, representing core implementation science principles and concepts that researchers should consider when designing implementation research
feature list: operation 3435

Impact framework
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 3300
application sub category: topic 3398
citation: j.mec.2019.e00089
citation: pmcid:PMC6462781
citation: pubmed:31011536
description: Python package for writing data analysis workflows to interpret microbial physiology.
feature list: operation_0337
feature list: operation 1812
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: readme.md
software version: 0.5.0
primary contact: Laboratory for Metabolic Systems Engineering

ImputeDistances
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0194
application sub category: topic 3293
application sub category: topic 3474
citation: https://doi.org/10.1101/744789
description: Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices | We introduce two highly accurate machine learning based distance imputation techniques. One of our approaches is based on matrix factorization (MatrixFactorization.py), and the other one is an autoencoder based deep learning technique (Autoencoder.py). We evaluate these two techniques on a collection of simulated and biological datasets, and show that our techniques are more accurate and robust than the best alternate technique for distance imputation. Moreover, our proposed techniques can handle substantial amount of missing data, to the extent where the best alternate method fails | (See the imports in both of the python files) | -python 3.5+ -easygui -pandas -numpy -matplotlib -seaborn -tensorflow -keras
feature list: operation_0557
feature list: operation 3478
feature list: operation 3557

Imread for multiple life science image file formats
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3344
application sub category: topic 3382
application sub category: topic 3934
description: MATLAB script for importing images and metadata using the LOCI Bioformats package.
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.7.0.0
primary contact: Christoph Moehl

ImtRDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Desktop application
application sub category: topic_0157
application sub category: topic 2885
application sub category: topic 3168
citation: s12864-019-5536-1
citation: pmcid:PMC6614062
citation: pubmed:31284879
description: Database and software for mitochondrial imperfect interspersed repeats annotation.
feature list: operation_0237
feature list: operation 3431
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.txt
primary contact: Konstantin Gunbin
primary contact: Viktor Shamansky

IndigoMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: INDIGO enables the integration of annotations for the exploration and analysis of newly sequenced microbial genomes.
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 1.1

InferAMP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2640
application sub category: topic 2885
application sub category: topic 3168
citation: F1000RESEARCH.19541.3
citation: pmcid:PMC6777010
citation: pubmed:31608148
description: Python web app for copy number inference from discrete gene-level amplification signals noted in clinical tumor profiling reports | Genome scale copy number inference from discrete reports of gene-level amplifications on somatic cancer NGS testing reports | InferAMP - inferring genome-wide amplicon boundaries from cancer NGS reports | Optimized for Foundation One reports from Foundation Medicine | A working version of the web implementation is at http://inferamp.org
license: MIT

InfernoRDN
type: SoftwareApplication
input: Peptide identification
  type: FormalParameter
  additional type: data_0945
  encoding format: format 3475
  encoding format: format 3620
  encoding format: format 3752
  encoding format: format 3758
output: Expression data
  type: FormalParameter
  additional type: data 2603
  encoding format: format 3752
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 3579
  encoding format: format 3603
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic 2269
application sub category: topic 3520
citation: btn217
citation: pmcid:PMC2692489
citation: pubmed:18453552
description: InfernoRDN can perform various downstream data analysis, data reduction, and data comparison tasks including normalization, hypothesis testing, clustering, and heatmap generation.
feature list: operation_0337
feature list: operation_0531
feature list: operation 2238
feature list: operation 2939
feature list: operation 3432
feature list: operation 3435
feature list: operation 3557
feature list: operation 3630
license: Apache-2.0

InfiniumPurify-R
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3360
application sub category: topic 3512
application sub category: topic 3518
citation: BTZ885
citation: pubmed:31769783
description: Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities. R package for DNA methylation analysis. R package for DNA methylation analysis The proposition of cancer cells in a tumor sample, named as tumor purity, is an intrinsic factor of tumor samples and has potentially great influence in variety of analyses including differential methylation, subclonal deconvolution and subtype clustering. InfiniumPurify is an integrated R pa ckage for est imatin g and accoun ting for tum or puri ty based on DNA methylation Infinium 450 k array data. InfiniumPurify has three main functions getPurity, InfiniumDMC and InfiniumClust, which could infer tumor purity, differential methylation analysis and tumor sample c luster accounting for estimated or user-provided tumor purities, respectively. The InfiniumPurify package provides a comprehensive analysis of tumor purity in cancer methylation research.
feature list: operation 3204
feature list: operation 3435
feature list: operation 3629

InfoMating
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic_0625
application sub category: topic 3307
citation: J.TPB.2019.11.002
citation: pubmed:31756362
description: Multi-model inference of non-random mating from an information theoretic approach. Non-random mating and Information Theory. mate choice, assortative mating, jmating, sexual selection, akaike. Relying on the informational partition of the non-random mating effects, and by modeling mate choice and competition by the mutual propensity parameters, it is possible to identify the necessary and sufficient conditions of random mating and from here, develop and connect different kinds of models producing different effects. These models can be used to generate inferences on the parameters of interest. The software InfoMating implements the methodology to do so
feature list: operation 3659

InsectBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic_0659
application sub category: topic 3673
citation: gkv1204
citation: pmcid:PMC4702856
citation: pubmed:26578584
description: Comprehensive genetic resource and analysis platform of insects.
feature list: operation_0524
feature list: operation_0525
feature list: operation 3216
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php

IntMTQ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3519
citation: btz932
citation: pmcid:PMC7178424
citation: pubmed:31834359
description: Platform-integrated mRNA Isoform Quantification. Integrated model for RNA-Seq based transcript quantification. IntMTQ is an integrative method combining isoform expressions from NanoString/Exon-array platforms to provide better quantification of RNA-Seq based transcript abundances. We provide the source code of paper Platform-integrated mRNA Isoform Quantification for bioinformatics submission
feature list: operation 2495
feature list: operation 3198
feature list: operation 3800
license: Apache-2.0

Intelli-NGS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2269
application sub category: topic 3168
application sub category: topic 3474
citation: https://doi.org/10.1101/2019.12.17.879403
description: Deep neural network-based artificial intelligence to delineate good and bad variant calls from IonTorrent sequencer data. Intelli-NGS:Intelligent NGS, a deep neural network-based artificial intelligence to delineate good and bad variant calls from IonTorrent sequencer data Preprint: DOI https://doi.org/10.1101/2019.12.17.879403
feature list: operation_0484
feature list: operation 3227
feature list: operation 3675

InterPep2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic_0166
application sub category: topic 2275
citation: https://doi.org/10.1101/813238
description: Global Peptide-Protein Docking with Structural Templates. Abstract Motivation Interactions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is time-consuming, and because of the disordered nature of the ligand, the interactions are especially difficult to predict through software, requiring specialized solutions. Although several prediction-methods exist, most are limited in performance or availability. Results InterPep2 is a freely available method for predicting the structure of peptide-protein interactions. We have previously shown that structural templates can be used to accurately predict peptide-protein binding sites, and that using templates from regular protein-protein interactions will increase the number of sites found
feature list: operation_0267
feature list: operation 2464
feature list: operation 2492
feature list: operation 3899
feature list: operation 3904

InterSpin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0593
application sub category: topic 3172
citation: ACSOMEGA.8B02714
citation: pmcid:PMC6648201
citation: pubmed:31459550
description: Integrated Supportive Webtools for Low- and High-Field NMR Analyses Toward Molecular Complexity | Description SpinLIMS Contact Others | Integrated supportive webtools for low- and high-field NMR analysis toward molecular complexities | SENsitivity improvement with Spectral Integration
feature list: operation 3215
feature list: operation 3637
feature list: operation 3642

InterVA-5
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3063
application sub category: topic 3305
application sub category: topic 3411
application sub category: topic 3418
citation: https://doi.org/10.1080/16549716.2019.1680068
citation: pmcid:PMC6818104
citation: pubmed:31648624
description: Adding Circumstances Of Mortality CATegories (COMCATs) to deaths investigated by verbal autopsy. files relating to evaluation of InterVA-5 software. Resources relating to InterVA-5 verbal autopsy software. Software for WHO verbal autopsy standards. InterVA provides the leading public-domain resources for interpreting verbal autopsy data. InterVA is a suite of computer models to facilitate interpreting VAs, and the latest versions and information are available on a public-domain basis from this site. This research is based at the Umeå Centre for Global Health Research, in northern Sweden, which also hosted the World Health Organization Collaborating Centre for Verbal Autopsy from 2012 to 2016.
feature list: operation 2409
feature list: operation 3503
license: GPL-3.0

InteractionTransformer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2269
application sub category: topic 3384
application sub category: topic 3474
citation: https://doi.org/10.1101/2019.12.15.877134
description: The Case for Sensible Extraction of Interactions in the Era of Machine Learning. Extract meaningful interactions from machine learning models to obtain machine-learning performance with statistical model interpretability. Welcome to InteractionTransformer. Welcome to the InteractionTransformer wiki!. What our package does not do: extract transformations in the data to add them to the design matrix. For those capabilities, please see the SAFE Transformer package (https://github.com/ModelOriented/SAFE). Our package does have an experimental feature that will iteratively call InteractionTransformer and SAFETransformer to develop multi-layer interactions/transformation models, but this is still under development.
feature list: operation_0321
feature list: operation 3659
license: MIT
software help: wiki

IonSpattern
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3172
application sub category: topic 3382
application sub category: topic 3520
citation: BTZ345
citation: pmcid:PMC6612871
citation: pubmed:31510675
description: Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues | Spatial Dirichlet Gaussian Mixture Model for single ion images | run W_matrix.R GMM.R k_DGMM.R S_DGMM.R first | run CpG_Sal_mouse brain.R to get results of CpG and Sal preconditioned mouse brain data
feature list: operation 3891

IsoCor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
additional type: Library
application sub category: topic 2259
application sub category: topic 3172
application sub category: topic 3955
citation: btz209
citation: pubmed:30903185
description: IsoCor is a scientific software dedicated to the correction of low- and high-resolution mass spectrometry (MS) data for naturally occuring isotopes. IsoCor corrects raw MS data (mass fractions) for naturally-occurring isotopes of all elements and purity of the isotopic tracer. The output of IsoCor is the isotopologue distribution of the molecule (i.e. the relative fractions of molecular entities differing only in the number of isotopic substitutions of the tracer). IsoCor also calculates the mean enrichment (i.e. the mean isotopic content in the molecule) in metabolites.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest

IsoPOPd
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0610
application sub category: topic 3315
citation: PEERJ.8018
citation: pmcid:PMC6855200
citation: pubmed:31737449
description: Another look at the eigenvalues of a population matrix model. Theoretical Population Modeling for Understanding Growth Rates. Visualizing how the growth rates responds to alterations in life history traits. Hanley B, Connelly P, & Dennis B. 2019. IsoPOPd: Interactive software to understand how elements in a population matrix model influence the asymptotic population growth rate [Software]. Cornell University Library eCommons Repository. doi: https://doi.org/10.7298/bcmg-7w08
feature list: operation 2426
feature list: operation 3435

IsobariQ
type: SoftwareApplication
input: Peptide identification
  type: FormalParameter
  additional type: data_0945
  encoding format: format 3713
output: Expression data
  type: FormalParameter
  additional type: data 2603
  encoding format: format 2332
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic 2269
application sub category: topic 3520
citation: pr1009977
citation: pubmed:21067241
description: IsobariQ is a program designed for use in quantitative mass spectrometry based proteomics. It is a novel tool for accurate quantification of IPTL, iTRAQ and TMT data, and currently, it is the only freely available tool to analyse IPTL data. It allows the user to examine proteomic data in detail and interactively through a graphical user interface. In addition, it provides the user with advanced statistical analysis, including recently published variance stabilising normalisation (VSN).
feature list: operation 3435
feature list: operation 3630
feature list: operation 3635
feature list: operation 3639
feature list: operation 3641
feature list: operation 3694
feature list: operation 3705
feature list: operation 3799
license: GPL-3.0

Isodyn
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3835
input: Mass spectrum
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3835
output: Mass spectrum
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3835
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3955
citation: 978-1-0716-0159-4 12
citation: bth412
citation: bti573
citation: btl484
citation: pubmed:15256408
citation: pubmed:16002431
citation: pubmed:17000750
citation: pubmed:31893378
description: “C++”-program simulating the dynamics of metabolites and their isotopic isomers in the central metabolic network using a corresponding kinetic model. Supports the final step of 13C assisted the fluxomic analysis: evaluation of metabolic fluxes consistent with a given mass isotopomer distribution. The previous steps are supported by Ramid, Midcor, Isoform.
feature list: operation 2426
license: Freeware
operating system: Linux
software help: isodyn
software version: 1.0

Isoform
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3835
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3835
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3172
application sub category: topic 3955
citation: 978-1-0716-0159-4 12
citation: pubmed:31893378
description: R-program that prepares the corrected mass spectra (supposed to be provided by Midcor) to the final step of the workflow of fluxomic analysis: simulation of dynamics of mass isotopomer distribution in a kinetic model.
feature list: operation 3214
license: Freeware
operating system: Linux
software help: ramidcor
software version: 0.0.1.0

IsomiR_Find
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic 2885
application sub category: topic 3577
citation: https://doi.org/10.1155/2019/6193673
citation: pmcid:PMC6699389
citation: pubmed:31467902
description: An Approach to Identify Individual Functional Single Nucleotide Polymorphisms and Isoform MicroRNAs | MicroRNAs (miRNAs) and single nucleotide polymorphisms (SNPs) play important roles in disease risk and development, especially cancer. Importantly, when SNPs are located in pre-miRNAs, they affect their splicing mechanism and change the function of miRNAs. To improve disease risk assessment, we propose an approach and developed a software tool, IsomiR_Find, to identify disease phenotype-related SNPs and isomiRs in individuals. Our approach is based on the individual's samples, with SNP information extracted from the 1000 Genomes Project. SNPs were mapped to pre-miRNAs based on whole-genome coordinates and then SNP-pre-miRNA sequences were constructed. Moreover, we developed matpred2, a software tool to identify the four splicing sites of mature miRNAs
feature list: operation_0331
feature list: operation_0463
feature list: operation_0484

JACKS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
citation: gr.238923.118
citation: pmcid:PMC6396427
citation: pubmed:30674557
description: Analysis package for processing counts from genome-wide CRISPR/Cas9 screens.
feature list: operation_0335
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
primary contact: F. Allen

JACOBI4
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic_0160
application sub category: topic 3315
application sub category: topic 3382
citation: https://doi.org/10.1101/803684
description: JACOBI4 software for multivariate analysis of biological data. JACOBI4 является проектом, разработанным для автоматизации статистического многомерного анализа биологических данных. Д.А. Полунин, И.А. Штайгер, В.М. Ефимов Разработка программного комплекса JACOBI 4 для многомерного анализа микрочиповых данных // Вестник НГУ т.12 Вып. 2. – Новосибирск: Редакционно-издательский центр НГУ, 2014. С. 90-98
feature list: operation 3629
feature list: operation 3659
feature list: operation 3891

JAL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
additional type: Web service
application sub category: topic_0176
application sub category: topic_0632
application sub category: topic 2275
citation: ACS.JCIM.8B00453
citation: pubmed:31140800
description: Characterization of Hydration Properties in Structural Ensembles of Biomolecules.
feature list: operation_0244
feature list: operation_0478
feature list: operation 2476
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: jal.html
primary contact: Chandra S. Verma
primary contact: Minh N. Nguyen

JAMP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0621
application sub category: topic_0632
application sub category: topic 2885
application sub category: topic 3056
application sub category: topic 3168
citation: PEERJ.PREPRINTS.3269V2
citation: peerj.preprints.3269v4
description: Assessing intraspecific genetic diversity from community DNA metabarcoding data. Estimating intraspecific genetic diversity from community DNA metabarcoding data. JAMP - Just Another Metabarcoding Pipeline. JAMP is a modular metabarcoding pipeline, integrating different functions from USEARCH, VSEARCH, CUTADAPT and other programs. The pipeline is run as an R package and automatically generates the needed folders and summary statistics
feature list: operation_0450
feature list: operation_0487
feature list: operation 3192
feature list: operation 3196
feature list: operation 3200

JOA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3168
citation: s12859-019-2698-4
citation: pmcid:PMC6408804
citation: pubmed:30849961
description: Joint Overlap Analysis (JOA) of multiple genomic interval sets. Takes n interval sets and finds overlapping intervals with no constraints on the given intervals.
feature list: operation 3501
feature list: operation 3798
is accessible for free: true
operating system: Linux
operating system: Mac
software help: JOA
primary contact: Burcak Otlu

JRgui
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0749
application sub category: topic 2258
citation: ACSOMEGA.7B01464
citation: pmcid:PMC6645593
citation: pubmed:31457399
description: A Python Program of Joback and Reid Method | Python GUI program for a quick estimation of physicochemical properties of molecules | A brief description of JRgui program: | By using the modern object-oriented programming language Python (e.g. tkinter and pandas modules) and a chemoinformatics open source library (RDKit), the classic Joback and Reid group contribution method was revisited and written into a graphical user interface program JRgui
feature list: operation 1812

JUDI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic_0769
application sub category: topic 3489
citation: btz956
citation: pmcid:PMC7868055
citation: pubmed:31882996
description: Bioinformatics Pipeline using JUDI. This repository contains the source code of JUDI, a workflow management system for developing complex bioinformatics software with many parameter settings. Bioinformatics pipeline: Just Do It!. JUDI - Bioinformatics Pipeline: Just Do It.
license: MIT

JabberDock
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0166
application sub category: topic_0176
application sub category: topic 2275
citation: acs.jctc.9b00474
citation: pmcid:PMC7007192
citation: pubmed:31390206
description: Protein Docking Using a Single Representation for Protein Surface, Electrostatics, and Local Dynamics | protein docking using a density-based descriptor for atoms charge and dynamics | JabberDock provides a mechanism to dock two protein STID maps together in conjunction with the POW engine and BioBox | Shipped with this version of JabberDock is a heavily stripped version of biobox containing the functions JabberDock requires. Please move the biobox folder into whatever directory you like (e.g. your home), just make sure it's in your pythonpath There is a readme file in the biobox folder containing instructions on requirements and installation instructions
feature list: operation_0387
feature list: operation_0482
feature list: operation 3899
license: GPL-3.0

Jaccard
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0610
application sub category: topic_0621
application sub category: topic 2269
application sub category: topic 3292
application sub category: topic 3301
citation: S12859-019-3118-5
citation: pmcid:PMC6929325
citation: pubmed:31874610
description: Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data. Test Similarity Between Binary Data using Jaccard/Tanimoto Coefficients. Calculate statistical significance of Jaccard/Tanimoto similarity coefficients for binary data.
feature list: operation 2238
license: GPL-2.0

Jalview
type: SoftwareApplication
input: Structure alignment
  type: FormalParameter
  additional type: data_0886
  encoding format: format 1476
input: Sequence alignment
  type: FormalParameter
  additional type: data_0863
  encoding format: format 1477
  encoding format: format 1915
  encoding format: format 1929
  encoding format: format 1938
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  encoding format: format 1947
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  encoding format: format 1982
  encoding format: format 1984
  encoding format: format 1997
  encoding format: format 3015
  encoding format: format 3016
  encoding format: format 3311
  encoding format: format 3313
  encoding format: format 3774
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
  encoding format: format 1929
  encoding format: format 1947
  encoding format: format 1948
  encoding format: format 1961
  encoding format: format 1982
  encoding format: format 1997
  encoding format: format 3015
  encoding format: format 3313
  encoding format: format 3464
  encoding format: format 3774
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 1915
  encoding format: format 2331
  encoding format: format 3466
  encoding format: format 3603
  encoding format: format 3604
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0080
application sub category: topic_0092
citation: btp033
citation: pmcid:PMC2672624
citation: pubmed:19151095
description: Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.
feature list: operation_0324
feature list: operation_0564
feature list: operation 3081
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: citation
software help: documentation
software help: faq
software help: training
software version: 2.11.5.1
primary contact: https://orcid.org/0000-0002-7865-7382

Janus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0593
application sub category: topic 3855
citation: acs.jctc.9b00182
citation: pubmed:31310719
description: Extensible open-source software package for adaptive quantum mechanics/molecular mechanics (QM/MM) Methods.
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: intro.html

Jasmine
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0659
application sub category: topic_0769
application sub category: topic 3170
citation: btz806
citation: pmcid:PMC7703784
citation: pubmed:31681943
description: a Java pipeline for isomiR characterization in miRNA-Seq Data. MOTIVATION:The existence of complex subpopulations of miRNA isoforms, or isomiRs, is well established. While many tools exist for investigating isomiR populations, they differ in how they characterize an isomiR, making it difficult to compare results across different tools. Thus, there is a need for a more comprehensive and systematic standard for defining isomiRs. Such a standard would allow investigation of isomiR population structure in progressively more refined sub-populations, permitting the identification of more subtle changes between conditions and leading to an improved understanding of the processes that generate these differences. RESULTS:We developed Jasmine, a software tool that incorporates a hierarchal framework for characterizing isomiR populations
feature list: operation 3198
feature list: operation 3435
feature list: operation 3792

Joint Multi-Modal Longitudinal Regression Classification
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
application sub category: topic 3360
application sub category: topic 3384
citation: tmi.2019.2958943
citation: pmcid:PMC7380699
citation: pubmed:31841400
description: Joint Multi-Modal Longitudinal Regression and Classification for Alzheimer's Disease Prediction. Code for Joint Multi-Modal Longitudinal Regression and Classification. Joint Multi-Modal Longitudinal Regression and Classification (JMMLRC) Estimator. This repository contains the code for performing a classification and a regression task at the same time on longitudinal data. This work has been applied to the ADNI dataset and has shown state-of-the-art performance in predicting patients with and without Alzheimer's Disease.
feature list: operation 3659

JointvetchMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: Aeschynomene evenia genomic data from the Legume Information System
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 2.1

K-TOPE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2830
citation: https://doi.org/10.1101/641787
description: General approach for identifying protein epitopes targeted by antibody repertoires using whole proteomes.
feature list: operation_0252
feature list: operation_0416
feature list: operation 3501
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://github.com/mlpaull/KTOPE/blob/master/KTOPE%20Usage%20Guide.docx
primary contact: Michael L. Paull
primary contact: Patrick S. Daugherty

KASPspoon
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic_0632
citation: btz004
citation: pmcid:PMC6735863
citation: pubmed:30624621
description: In vitro and in silico PCR analysis tool for high-throughput SNP genotyping.
feature list: operation_0282
feature list: operation_0308
feature list: operation 3196
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: KASPspoon-Manual-converted.pdf
primary contact: Dr. Shafik D. Ibrahim

KBCommons
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0659
application sub category: topic 3172
application sub category: topic 3173
application sub category: topic 3298
citation: S12864-019-6287-8
citation: pmcid:PMC6923931
citation: pubmed:31856718
description: a universal framework for multi-omics data integration and biological discoveries. Towards this, we have expanded our in-house developed Soybean Knowledge Base (SoyKB), a comprehensive all-inclusive web resource for soybean to other organisms via Knowledge Base Commons (KBCommons) without the need for reinventing the wheel. Advancement of next generation sequencing and high-throughput technologies has resulted in generation of multi-level of 'OMICS' data for many organisms
feature list: operation 2422
feature list: operation 2495
feature list: operation 2939
feature list: operation 2940

KBbox
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0202
application sub category: topic_0602
application sub category: topic 3375
citation: ACS.JCIM.9B00485
citation: pubmed:31381336
description: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding | KBbox is developed to be of use to researchers interested in applying these methods in their work. To help with this, KBbox provides an updated list of examples of published work, along with detailed tutorials to guide less experienced researchers

KDDANet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0202
application sub category: topic_0602
application sub category: topic 2840
citation: https://doi.org/10.1101/749762
description: Novel computational framework for systematic uncovering hidden gene interactions underlying known drug-disease associations | A computational framework for uncovering hidden gene interactions underlying Known Drug-Disease Associations (KDDAs) | To use KDDANet, please refer to the instructions in manual.txt in this subdirectory | This software identifies the hidden gene interactions and modules underlying KDDAs through implementing minimum cost optimization and graph clustering on a unified flow network model
feature list: operation 3501
license: GPL-3.0

KETOS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2640
application sub category: topic 3263
application sub category: topic 3474
citation: JOURNAL.PONE.0223010
citation: pmcid:PMC6776354
citation: pubmed:31581246
description: A training and deployment platform based on Docker, OMOP-CDM, and FHIR Web Services. BACKGROUND AND OBJECTIVE:To take full advantage of decision support, machine learning, and patient-level prediction models, it is important that models are not only created, but also deployed in a clinical setting. The KETOS platform demonstrated in this work implements a tool for researchers allowing them to perform statistical analyses and deploy resulting models in a secure environment. METHODS:The proposed system uses Docker virtualization to provide researchers with reproducible data analysis and development environments, accessible via Jupyter Notebook, to perform statistical analysis and develop, train and deploy models based on standardized input data. The platform is built in a modular fashion and interfaces with web services using the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) standard to access patient data
feature list: operation 2422
feature list: operation 3435
feature list: operation 3659

KOFFI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0821
application sub category: topic 3068
application sub category: topic 3489
citation: BAZ101
citation: pmcid:PMC6790968
citation: pubmed:31608948
description: new binding kinetics database and its integration in an open-source binding analysis software. Kinetics OF Featured Interactions. KOFFI-DB (???) is an article based database for kinetic constants of biomolecular interactions. We focused on interactions between DNA, RNA, proteins and chemical compounds. All datapoints were manually annotated and reviewed based on open source articles available on Europe PMC
feature list: operation_0306
feature list: operation 2421
feature list: operation 3778

KOREF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 3673
citation: GIZ125
citation: pmcid:PMC6889754
citation: pubmed:31794015
description: Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information. The first Korean Reference Genome. KOREF_S means KOREF_Single.
feature list: operation_0523
feature list: operation_0524
feature list: operation_0525
feature list: operation 3216
feature list: operation 3228

KPDGUI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3421
citation: J.COMPBIOMED.2019.03.013
citation: pmcid:PMC6538268
citation: pubmed:31054501
description: KPDGUI (Kidney Paired Donation Graphical User Interface) - interactive application for optimization and management of a virtual kidney paired donation program.
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Mathieu Bray

KPHMMER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0160
application sub category: topic_0602
application sub category: topic 3407
citation: https://doi.org/10.1101/636290
description: Hidden Markov Model generator for detecting KEGG PATHWAY-specific genes.
feature list: operation 3092
feature list: operation 3501
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Hirotaka Suetake

KRAB ZNF explorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3295
citation: btz624
citation: pubmed:31392309
description: Online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas.
feature list: operation_0420
feature list: operation 2495
feature list: operation 3800
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: KRAB ZNF
primary contact: Urszula Oleksiewicz

KRASi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0602
application sub category: topic 3379
citation: https://doi.org/10.1101/769703
description: Defining and targeting adaptations to oncogenic KRASG12C inhibition using quantitative temporal proteomics | ABSTRACT Covalent inhibitors of the KRAS G12C oncoprotein have recently been developed and are being evaluated in clinical trials. Resistance to targeted therapies is common and likely to limit long-term efficacy of KRAS inhibitors (KRASi). To identify pathways of adaptation to KRASi and to predict drug combinations that circumvent resistance, we used a mass spectrometry-based quantitative temporal proteomics and bioinformatics workflow to profile the temporal proteomic response to KRAS G12C inhibition in pancreatic and lung cancer 2D and 3D cellular models. We quantified 10,805 proteins across our datasets, representing the most comprehensive KRASi proteomics effort to date. Our data reveal common mechanisms of acute and long-term response between KRAS G12C -driven tumors
feature list: operation 2436
feature list: operation 3799
operating system: Linux
operating system: Mac
operating system: Windows

KSEA App
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web application
application sub category: topic_0154
application sub category: topic 3068
citation: btx415
citation: pmcid:PMC5860163
citation: pubmed:28655153
description: Kinase-Substrate Enrichment Analysis (KSEA) App - web-based tool for kinase activity inference from quantitative phosphoproteomics.
feature list: operation_0337
feature list: operation 3501
feature list: operation 3799
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://casecpb.shinyapps.io/ksea/_w_e64191f6/session/1988eac24ab1e3de94e0244530450cdf/download/Manual
software help: KSEAapp.pdf
software help: Overview.html
primary contact: Danica D. Wiredja
primary contact: Mark R. Chance

Kaptive
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 2830
application sub category: topic 3301
application sub category: topic 3305
application sub category: topic 3673
citation: https://doi.org/10.1101/869370
description: Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Kaptive reports information about surface polysaccharide loci for Klebsiella and Acinetobacter baumannii genome assemblies. You can also run a graphical version of Kaptive via this web interface (source code). Given a novel genome and a database of known loci (K, O or OC), Kaptive will help a user to decide whether their sample has a known or novel locus. It carries out the following for each input assembly:. Kaptive is a tool for bacterial surface polysaccharide locus typing and variant evaluation. It takes one or more pre-assembled genomes and for each finds the best matching locus from a reference database. References for Klebsiella pneumoniae species complex and Acinetobacter baumannii are available in Kaptive's web interface
feature list: operation_0525
feature list: operation 2421
feature list: operation 3431
feature list: operation 3840
license: GPL-3.0

KataegisPortal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0634
application sub category: topic 2830
application sub category: topic 3411
application sub category: topic 3518
application sub category: topic 3673
citation: JMEDGENET-2019-106418
citation: pubmed:31862729
description: Multiregion whole-genome sequencing depicts intratumour heterogeneity and punctuated evolution in ovarian clear cell carcinoma. An R package for detecting and visualizing Kataegis events. KataegisPortal is an R package that provides utilities to detect and visualize the Kataegis events from single nucleotide variants (SNVs)
feature list: operation_0337
feature list: operation 3454
feature list: operation 3891

KeyPathwayMiner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3295
application sub category: topic 3518
citation: 978-1-4939-9873-9 14
citation: pubmed:31583639
description: De Novo Pathway Enrichment with KeyPathwayMiner. (17E1EF77D1E66C1CFE344BDA3D7945B0). Given a biological network and a set of case-control studies, KeyPathwayMiner efficiently extracts all maximal connected sub-networks. These sub-networks contain the genes that are mainly dysregulated, e.g., differentially expressed, in most cases studied.
feature list: operation 3083
feature list: operation 3439
feature list: operation 3501

KinVis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 3517
author: Dr. Ehsan Ullah
citation: bty1028
citation: pmcid:PMC6931347
citation: pubmed:30590437
description: Visualization tool to detect cryptic relatedness in genetic datasets.
feature list: operation 3196
feature list: operation 3208
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Dr. Ehsan Ullah
primary contact: Dr. Halima Bensmail

Kirchhoff polynomials
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0204
application sub category: topic_0820
application sub category: topic_0821
application sub category: topic 3314
application sub category: topic 3570
citation: https://doi.org/10.1101/868323
description: Efficient Manipulation and Generation of Kirchhoff Polynomials for the Analysis of Non-equilibrium Biochemical Reaction Networks. Efficient manipulation and compact generation of expressions of Kirchhoff polynomials
feature list: operation_0270
feature list: operation 2995

KisSplice
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic 3170
application sub category: topic 3308
citation: 1471-2105-13-s6-s5
citation: pmcid:PMC3358658
citation: pubmed:22537044
description: KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome.
feature list: operation 3227
feature list: operation 3258

Kmasker
type: SoftwareApplication
input: Sequence set
  type: FormalParameter
  additional type: data_0850
  encoding format: format 1929
input: Sequence search results
  type: FormalParameter
  additional type: data_0857
  encoding format: format 1333
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1929
input: Annotation track
  type: FormalParameter
  additional type: data 3002
  encoding format: format 1975
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
output: Position frequency matrix
  type: FormalParameter
  additional type: data 1361
  encoding format: format 3665
output: Position frequency matrix
  type: FormalParameter
  additional type: data 1361
  encoding format: format 3665
output: Annotation track
  type: FormalParameter
  additional type: data 3002
  encoding format: format 1975
output: Annotation track
  type: FormalParameter
  additional type: data 3002
  encoding format: format 1975
output: Position frequency matrix
  type: FormalParameter
  additional type: data 1361
  encoding format: format 3665
output: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
output: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
output: Sequence features metadata
  type: FormalParameter
  additional type: data 2914
  encoding format: format 1975
output: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
output: Annotation track
  type: FormalParameter
  additional type: data 3002
  encoding format: format 1975
output: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 1929
output: Score
  type: FormalParameter
  additional type: data 1772
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web service
application sub category: topic_0157
application sub category: topic_0780
application sub category: topic_0797
application sub category: topic 3511
author: https://orcid.org/0000-0001-5444-9282
author: https://orcid.org/0000-0002-2177-8781
author: https://orcid.org/0000-0003-1073-6719
author: Markus Schwalbe
citation: TPJ.14645
citation: pubmed:31823436
contributor: https://orcid.org/0000-0002-2177-8781
contributor: Markus Schwalbe
description: Kmasker plants is a tool for the automatic detection of sequence regions with meaningful k-mer characteristics. This can be sequences with highly abundant k-mer patterns (repeats), regions with diverging k-mer patterns between two studied WGS samples or segments with high target specificity.
feature list: operation_0237
feature list: operation_0379
feature list: operation_0463
feature list: operation 2428
feature list: operation 2451
feature list: operation 3472
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: INSTALL.md
software help: README.md
software version: 1.1.0
software version: 1.1.1
primary contact: https://orcid.org/0000-0001-5444-9282
primary contact: https://orcid.org/0000-0003-1073-6719

Kmasker plants
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic_0780
application sub category: topic 3673
application sub category: topic 3912
citation: TPJ.14645
citation: pubmed:31823436
description: A tool for assessing complex sequence space in plant species. Kmasker - a tool for masking and exploring of sequences from plant species. a versatile tool for masking and exploring of sequences from plant species. Kmasker plants is a tool for the automatic detection of sequence regions with meaningful k-mer characteristics. This can be sequences with highly abundant k-mer patterns (repeats), regions with diverging k-mer patterns between two studied WGS samples or segments with high target specificity. The installation instructions are available at: INSTALL.md. There, you find our list of requirements of external tools. Please make sure, that these are in your PATH environemnt if you installed from source. If not please specify them in the 'etc/kmasker.config' file. Kmasker uses an interal repository for reuse of kindex structures.
feature list: operation_0368
feature list: operation_0525
feature list: operation 3196
feature list: operation 3211
feature list: operation 3472
license: GPL-3.0

KnockTF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3170
application sub category: topic 3518
citation: gkz881
citation: pmcid:PMC6943067
citation: pubmed:31598675
description: A comprehensive human gene expression profile database with knockdown/knockout of transcription factors. We develop a comprehensive human gene expression profile database with TF knockdown/knockout (KnockTF), which provides a large number of available resources of human gene expression profile datasets associated with TF knockdown/knockout and annotates TFs and their target genes in a tissue/cell type-specific manner
feature list: operation_0315
feature list: operation 2436
feature list: operation 2942

Knot_pull
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
citation: btz644
citation: pmcid:PMC9883683
citation: pubmed:31504154
description: Knot_pull-python package for biopolymer smoothing and knot detection | Python module for knot-like structure detection in biological molecules | KnotPull - a simplifier for 3D structures | KnotPull reduces a user provided 3D structure, to simplify it, while preserving the topology of the chain. It has been successfully used for knot detection in proteins and chromatin chains
feature list: operation 3890
license: GPL-3.0

Knoto-ID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0091
application sub category: topic_0736
application sub category: topic 3315
citation: bty365
citation: pubmed:29722808
description: Tool to study the entanglement of open protein chains using the concept of knotoids.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Julien Dorier

KnowPulse
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0625
citation: FPLS.2019.00965
citation: pmcid:PMC6690010
citation: pubmed:31428111
description: A Web-Resource Focused on Diversity Data for Pulse Crop Improvement | Welcome to the Public Portal for the University of Saskatchewan Pulse Crop Research Group | ◼ View other species of interest | ◼ View other bioinformatics tools
feature list: operation_0282
feature list: operation 3196
feature list: operation 3232

KoBra
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3314
application sub category: topic 3315
application sub category: topic 3318
citation: JCC.25857
citation: pubmed:31120584
description: Rate constant method for prediction of the diffusion of sorbates inside nanoporous materials at different loadings.
feature list: operation 1812
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: download
primary contact: Panagiotis D. Kolokathis

KofamKOALA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0160
application sub category: topic_0602
application sub category: topic_0621
application sub category: topic_0623
citation: btz859
citation: pmcid:PMC7141845
citation: pubmed:31742321
description: KEGG ortholog assignment based on profile HMM and adaptive score threshold. KofamKOALA - KEGG Orthology Search. K number assignment based on KO-dependent scoring criteria. KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam (a customized HMM database of KEGG Orthologs (KOs)). K number assignments with scores above the predefined thresholds for individual KOs are more reliable than other proposed assignments. Such high score assignments are highlighted with asterisks '*' in the output. The K number assignments facilitate the interpretation of the annotation results by linking the user's sequence data to the KEGG pathways and EC numbers.
feature list: operation_0533
feature list: operation 2421
feature list: operation 3092

KrakenUniq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0637
application sub category: topic 3174
application sub category: topic 3324
application sub category: topic 3673
application sub category: topic 3837
citation: JOURNAL.PCBI.1006863
citation: pmcid:PMC6897419
citation: pubmed:31756192
description: Identification and quantitation of clinically relevant microbes in patient samples.
feature list: operation 2428
feature list: operation 3460
feature list: operation 3472
feature list: operation 3799
license: MIT

KronRLS-MKL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3336
application sub category: topic 3474
citation: s12859-016-0890-3
citation: pmcid:PMC4722636
citation: pubmed:26801218
description: Matlab implementation of the Kronecker Regularized Least Squares with multiple kernels algorithm.
feature list: operation_0272
feature list: operation_0303
feature list: operation 2949
is accessible for free: true
operating system: Linux
operating system: Mac
software help: README.md
primary contact: André C. A. Nascimento

KymoButler
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2229
application sub category: topic 3382
application sub category: topic 3474
citation: ELIFE.42288
citation: pmcid:PMC6692109
citation: pubmed:31405451
description: Deep learning software for automated kymograph analysis | The AI that analyses your kymographs | The AI that analyses your kymograph | Easy drag and drop software under http://kymobutler.deepmirror.ai | Download KymoButler.nb and open it in Mathematica. Run the first cell to download the necessary neural networks and the KymoButler package. The use the function KymoButler[] to analyse your kymographs
feature list: operation_0337
feature list: operation 3216
feature list: operation 3435
license: GPL-3.0

L1EM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: btz724
citation: pmcid:PMC8215917
citation: pubmed:31584629
description: A tool for accurate locus specific LINE-1 RNA quantification. Estimate locus specific human LINE-1 expression. git clone https://github.com/wmckerrow/L1EM. git (https://git-scm.com/book/en/v2/Getting-Started-Installing-Git). anaconda (https://docs.anaconda.com/anaconda/install/). If necessary, you can specify the path for bwa and samtools in the run_L1EM.sh script. You must use samtools >=1.0. Early version of pysam will not work. I highly recommend that you use bwa 0.7.17. Earlier versions may differ in how they write the XA tag. This will lead to inaccurate results without throwing an error
feature list: operation 2495
feature list: operation 3192
feature list: operation 3198
feature list: operation 3799
license: GPL-3.0

LABiocin database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0154
application sub category: topic 3293
application sub category: topic 3361
citation: J.IJANTIMICAG.2019.07.012
citation: pubmed:31374334
description: A new database designed specifically for Lactic Acid Bacteria bacteriocins | Bacteriocins from lactic acid bacteria (LAB) are successfully applied as natural alternatives to food preservation and to antibiotics; however, information on these antimicrobial peptides (AMPs) is scattered through the literature and databases. Therefore, we developed the LABiocin database, a specialized database on LAB bacteriocins. The database was stored and compiled using MySQL with NetBeans IDE as the platform. Important data are compiled, including bacteriocin name, class, amino acids and nucleic acid sequences, if available. Target microorganisms, origin, status of the producing strains and their culture conditions and extraction and purification methods are also included in this new database. A phylogenetic tree for the mature peptide bacteriocin sequences has also been created

LARMD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0176
application sub category: topic 2640
application sub category: topic 3336
citation: BBZ141
citation: pubmed:31799600
description: Integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor. Protein dynamics is central to all biological processes, including signal transduction, cellular regulation and biological catalysis. Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein function, which is particularly relevant to drug discovery. Hence, a wide range of computational tools have been designed to investigate the important dynamic information in proteins. However, performing and analyzing protein dynamics is still challenging due to the complicated operation steps, giving rise to great difficulty, especially for nonexperts. Moreover, there is a lack of web protocol to provide online facility to investigate and visualize ligand-driven protein dynamics
feature list: operation 2476
feature list: operation 2495

LAS database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3325
citation: j.ando.2012.05.001
citation: pubmed:22682917
description: Liege Acromegaly Survey (LAS) database includes anonymous historical and prospective data on liege acromegaly patients, pathophysiology, clinical features, responses to therapy and long term outcomes of acromegaly.
primary contact: Patrick Petrossians

LASHiS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0769
application sub category: topic 3384
application sub category: topic 3444
citation: https://doi.org/10.1101/759217
description: Longitudinal Automatic Segmentation of Hippocampal Subfields (LASHiS) using Multi-Contrast MRI | LASHiS was loosely adapted from the ANTs Longitudinal Cortical Thickness pipeline https://github.com/ANTsX/ANTs/ The ASHS_TSE image slice direction should be z. In other words, the dimension of ASHS_TSE image should be 400x400x30 or something like that, not 400x30x400
feature list: operation 3435
feature list: operation 3891
license: GPL-2.0

LASSI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic 2229
application sub category: topic 3047
citation: JOURNAL.PCBI.1007028
citation: pmcid:PMC6822780
citation: pubmed:31634364
description: A lattice model for simulating phase transitions of multivalent proteins. Many biomolecular condensates form via spontaneous phase transitions that are driven by multivalent proteins. These molecules are biological instantiations of associative polymers that conform to a so-called stickers-and-spacers architecture. The stickers are protein-protein or protein-RNA interaction motifs and or domains that can form reversible, non-covalent crosslinks with one another. Spacers are interspersed between stickers and their preferential interactions with solvent molecules determine the cooperativity of phase transitions. Here, we report the development of an open source computational engine known as LASSI (LAttice simulation engine for Sticker and Spacer Interactions) that enables the calculation of full phase diagrams for multicomponent systems comprising of coarse-grained representations of multivalent proteins.
feature list: operation 2949
feature list: operation 3454
feature list: operation 3893

LAVA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0622
application sub category: topic_0749
application sub category: topic_0781
application sub category: topic 3676
citation: https://doi.org/10.1101/2019.12.17.879320
description: a streamlined visualization tool for longitudinal analysis of viral alleles. LAVA: Longitudinal Analysis of Viral Alleles. LAVA analyzes and visualizes minor allele variants in longitudinal sequence data. LAVA takes a reference fasta (normally representing the first sample in your longitudinal analysis), fastq files (for every sample in your analysis), and a metadata sheet (providing information on what day or passage each sample was collected). Output will be displayed as an interactive graph in your web browser. LAVA will only work on Mac and Linux machines
feature list: operation_0337
feature list: operation 1812
feature list: operation 3192
feature list: operation 3227
license: GPL-3.0

LAmbDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3474
citation: btz295
citation: pmcid:PMC6853662
citation: pubmed:31038689
description: Label Ambiguous Domain Adaptation (LAmbDA) - species- and dataset-independent transfer learning framework (LAmbDA) to train models on multiple datasets.
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Jie Zhang
primary contact: Kun Huang

LBEEP
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
output: Sequence
  type: FormalParameter
  additional type: data 2044
  encoding format: format 2310
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
author: https://orcid.org/0000-0001-5145-0384
citation: omi.2015.0095
citation: pubmed:26406767
description: LBEEP (Linear B-Cell Exact Epitope Predictor) is a perl based open source tool for the prediction of Linear B-cell epitopes. Please refer the article tilted "Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-based Feature Descriptor" for more deatils.
feature list: operation_0252
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: LBEEP

LCA-CNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3382
application sub category: topic 3474
citation: J.NEUNET.2019.10.009
citation: pubmed:31683145
description: Learning Cascade Attention for fine-grained image classification. Code for paper "Learning Cascade Attention for Fine-grained Image Classification", which currently under review at Elsevier Journal of Neural Networks(NN). Train/test split for CUB-200-2011 dataset. Rotate training set for data augmentation.
feature list: operation 3359

LD-annot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3518
application sub category: topic 3673
citation: FGENE.2019.01192
citation: pmcid:PMC6889475
citation: pubmed:31850063
description: A Bioinformatics Tool to Automatically Provide Candidate SNPs With Annotations for Genetically Linked Genes. Practical program to annotate candidate polymorphism using annotations for genes in genetic linkage in the specific experiment. A bioinformatics tool to automatically provide annotations for genes included in DNA blocks in linkage disequilibrium with candidate SNPs. LD-annot estimates experiment-specific linkage disequilibrium to delineate regions genetically linked to each genetic markers from a list of polymorphisms (most often candidate SNPs from GWAS) and provide coordinates and annotations for genes included or overlapping such regions. Email: jprunier.1@gmail.com or arnaud.droit@crchudequebec.ulaval.ca
feature list: operation_0488
feature list: operation 3196
feature list: operation 3216
feature list: operation 3661
license: GPL-3.0

LDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic 3047
application sub category: topic 3172
application sub category: topic 3314
application sub category: topic 3520
citation: S41597-019-0305-1
citation: pmcid:PMC6882832
citation: pubmed:31780665
description: A database of high-resolution MS/MS spectra for lichen metabolites. The Global Natural Product Social Molecular Networking (GNPS) site creates a community for natural product researchers working with mass spectrometry data. MassIVE Datasets : Documentation : Forum : Contact. "2,8-Dimethyl-5,7-dimethoxychromone". "5,7-Dihydroxy-2,6,8-trimethylchromone".
feature list: operation_0337
feature list: operation 3646
feature list: operation 3801
feature list: operation 3803

LDPC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0632
citation: https://doi.org/10.1101/770032
description: Improved read/write cost tradeoff in DNA-based data storage using LDPC codes | LDPC codes for Illumina sequencing-based DNA storage
feature list: operation 3192

LDassoc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0102
application sub category: topic 3305
application sub category: topic 3517
citation: btx561
citation: pmcid:PMC6030966
citation: pubmed:28968746
description: Tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation.
feature list: operation_0487
feature list: operation_0488
feature list: operation 3196
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Mitchell J. Machiela

LDmotif
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0160
application sub category: topic_0621
application sub category: topic 3474
citation: btz703
citation: pmcid:PMC7703752
citation: pubmed:31584626
description: Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs. Source code for LD motif detection. In this repository, we uploaded the necessary files to set up and environment to predict the LD motif from input sequence. We also have a server for LD motif predition : https://www.cbrc.kaust.edu.sa/ldmf/. Users need to run scripts after changing the value of input parameters. The deatils of each parameter is also provide. The code is shared in the folder "src". All external jars are shared in the folder "ExternalJar_Required" There are two files that should be used for Amino Acid index. These files are also shared.
feature list: operation_0238
feature list: operation_0239
feature list: operation_0478

LEMON
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0114
application sub category: topic 3168
application sub category: topic 3174
application sub category: topic 3175
application sub category: topic 3697
citation: S12859-019-3301-8
citation: pmcid:PMC6933643
citation: pubmed:31881904
description: A method to construct the local strains at horizontal gene transfer sites in gut metagenomics. It is a software to reconstruct the HGT inserted local strain. It is a software takes use of existing shotgun NGS datasets to detect HGT breakpoints, identify the transferred genome segments, and reconstructs the inserted local strain. usage: python LEMON/Scripts/get_raw_bkp.py [options]. git clone --recursive https://github.com/lichen2018/hgt-detection.git
feature list: operation_0495
feature list: operation 3228
feature list: operation 3359
feature list: operation 3802

LESSeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3512
application sub category: topic 3518
citation: https://doi.org/10.1101/841494
description: Local event-based analysis of alternative splicing using RNA-Seq data. Local Event-based analysis of alternative Splicing using RNA-Seq. The Local Event-based analysis of alternative Splicing using RNA-Seq (or LESSeq) is a Linux-based processing pipeline for analyzing alternative splicing events from RNA-Seq data
feature list: operation 2499
feature list: operation 3196
feature list: operation 3680
feature list: operation 3800
license: MIT

LFAQ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: acs.analchem.8b03267
citation: pubmed:30525483
description: Algorithm for label-free absolute protein quantification, which can correct the biased MS intensities using the predicted peptide quantitative factors for all identified peptides.
feature list: operation 2929
feature list: operation 3631
feature list: operation 3634
is accessible for free: true
license: Artistic-2.0
operating system: Windows
software help: User Guide for LFAQ.pdf
primary contact: Cheng Chang
primary contact: Zhiqiang Gao

LFQ-Analyst
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3520
citation: ACS.JPROTEOME.9B00496
citation: pubmed:31657565
description: An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free Proteomics Data Preprocessed with MaxQuant. A tool for analysing label-free quantitative proteomics dataset https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst/. LFQ-Analyst: An easy-to-use interactive web-platform to analyze and visualize proteomics data preprocessed with MaxQuant. LFQ-Analyst is an easy-to-use, interactive web application developed to perform differential expression analysis with “one click” and to visualize label-free quantitative proteomic datasets preprocessed with MaxQuant. LFQ-Analyst provides a wealth of user-analytic features and offers numerous publication-quality result output graphics and tables to facilitate statistical and exploratory analysis of label-free quantitative datasets
feature list: operation 2939
feature list: operation 3435
feature list: operation 3557
feature list: operation 3634
feature list: operation 3891
license: GPL-3.0
software help: LFQ-Analyst manual.pdf

LFastqC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3071
application sub category: topic 3168
citation: JOURNAL.PONE.0224806
citation: pmcid:PMC6855649
citation: pubmed:31725736
description: A lossless non-reference-based FASTQ compressor. Contribute to sya12005/LFastqC development by creating an account on GitHub. You can’t perform that action at this time

LGE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3306
application sub category: topic 3384
application sub category: topic 3444
citation: JOURNAL.PCBI.1007421
citation: pmcid:PMC6837623
citation: pubmed:31658247
description: Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort. An automated script for extracting the scar area, entropy, components, transmurality, radiality and interface length from short axis late gadolinium enhanced cardiac MRI images in nifti format. This repository provides a script that creates a list of metrics quantifying a scar pattern seen in a cardiac short axis late gadolinium enhanced MRI image. The metrics provided are. area - The total area of the scar. radiality - The angular extent of the LGE pattern, with values between 0 and 1. A score of 1 indicates that scars are present in a full 360 degree pattern with respect to the centre of the blood pool, wheras 0 indicates no angular extent of scar.
feature list: operation_0244
feature list: operation_0455
feature list: operation 2426

LGG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic 2269
application sub category: topic 2640
citation: noz191
citation: pmcid:PMC7229246
citation: pubmed:31621885
description: An independently validated survival nomogram for lower grade glioma. BACKGROUND:Gliomas are the most common primary malignant brain tumor. Diffuse low-grade and intermediate-grade gliomas, which together comprise the lower-grade gliomas [LGG] (WHO grades II and III), present a therapeutic challenge to physicians due to the heterogeneity of their clinical behavior. Nomograms are useful tools for individualized estimation of survival. This study aimed to develop and independently validate a survival nomogram for patients with newly diagnosed LGG. METHODS:Data were obtained for newly diagnosed LGG patients from The Cancer Genome Atlas (TCGA) and the Ohio Brain Tumor Study (OBTS) with the following variables: tumor grade (II or III), age at diagnosis, sex, Karnofsky Performance Status (KPS), and molecular subtype (IDH mutant with 1p 19q codeletion [IDHmut-codel], IDH mutant without 1p 19q codeletion [IDHmut-non-codel], IDH wild-type [IDHwt])
feature list: operation 2428
feature list: operation 3503
feature list: operation 3659

LIBR MOCD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3489
citation: https://doi.org/10.1101/731331
description: LIBR Methamphetamine and Opioid Cue Database (LIBR MOCD) | Repository for the LIBR Meth Opioid Cue Reactivity Database | This project contains two folders:

LIDC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0605
application sub category: topic_0621
application sub category: topic 2640
application sub category: topic 3384
application sub category: topic 3452
citation: PEERJ.PREPRINTS.27378V2
description: Standardized representation of the LIDC annotations using DICOM. Scripts for converting TCIA LIDC-IDRI collection derived data into standard DICOM representation from project-specific XML format. This repository contains the script used to convert the TCIA LIDC-IDRI XML representation of nodule annotations and characterizations into the DICOM Segmentation object (for annotations) and DICOM Structured Reporting objects (for nodule characterizations). pylidc is an Object-relational mapping (using SQLAlchemy) for the data provided in the LIDC dataset. This means that the data can be queried in SQL-like fashion, and that the data are also objects that add additional functionality via functions that act on instances of data obtained by querying for particular attributes.
feature list: operation_0224
feature list: operation 3435
feature list: operation 3553

LIGNIN-KMC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0780
application sub category: topic 3314
application sub category: topic 3315
citation: CHEMRXIV.8178722
description: Toolkit for Simulating Lignin Biosynthesis.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

LIMES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0091
citation: BTZ911
citation: pubmed:31804675
description: A tool for comparing species partition. We are pleased to announce the launch of Limes!.

LINbase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0780
application sub category: topic 3810
citation: https://doi.org/10.1101/752212
description: A Web service for genome-based identification of microbes as members of crowdsourced taxa | Abstract The development of next generation and third generation DNA sequencing technologies in combination with new efficient algorithms allows scientists to economically, quickly, and precisely identify microbes at all taxonomic levels and even attribute pathogen isolates to specific disease outbreaks. However, current taxonomic practice has not kept up with the sequencing revolution and continues to rely on cumbersome journal publications to describe new species. Here we introduce a Web service that allows any user to genomically circumscribe any monophyletic group of bacteria as a taxon and associate with each taxon a name and short description. Any other user can immediately identify their unknown microbe as a member of any of these crowdsourced taxa using gene or genome sequences. The Web service is called LINbase
feature list: operation 3840

LION-web
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0153
application sub category: topic 3306
citation: GIZ061
citation: pmcid:PMC6541037
citation: pubmed:31141612
description: Web-based ontology enrichment tool for lipidomic data analysis.
feature list: operation_0335
feature list: operation 3501
feature list: operation 3629
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0001-7311-3821

LIQUID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0153
application sub category: topic_0154
application sub category: topic_0780
citation: btx046
description: Software for identifying lipids in LC-MS/MS-based lipidomics data.
is accessible for free: true
license: Apache-2.0
operating system: Windows
software help: README.md
software help: LIQUID installation operation.pdf

LLCT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0121
application sub category: topic_0625
application sub category: topic 3172
application sub category: topic 3518
citation: S12859-019-3221-7
citation: pmcid:PMC6902471
citation: pubmed:31822265
description: Longitudinal linear combination test for gene set analysis. LLCT is a two-step self-contained gene-set analysis method which is developed to handle multiple longitudinal outcomes. Analysis of within-subject variation in the first step is followed by examining the between-subject variation utilizing Linear Combination Test (LCT) in the second step. This method is also applicable in analysis of time-course microarray data
feature list: operation 2436
feature list: operation 3196
feature list: operation 3463
feature list: operation 3659

LM-GlycomeAtlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0203
application sub category: topic 3172
application sub category: topic 3292
application sub category: topic 3336
application sub category: topic 3382
application sub category: topic 3518
citation: ACS.JPROTEOME.0C00907
citation: MOLECULES24162962
citation: pmcid:PMC6719194
citation: pubmed:31443278
citation: pubmed:33657805
description: A Novel Visualization Tool for Lectin Microarray-Based Glycomic Profiles of Mouse Tissue Sections | LM-GlycomeAtlas v.1.0 is a web tool visualizing the data from Lectin Microarray analyses using 45 lectins by the Kuno Laboratory at AIST | This work was supported by a project for utilizing glycans in the development of innovative drug discovery technologies in the project focused on developing key technology for discovering and manufacturing drugs for next-generation treatment and diagnosis from the Japan Agency for Medical Research and Development (AMED) | CFG(Consortium for Functional Glycomics) Glycan Profilling data | Mapping data of human serum data was from Dr. Shunji Natsuka of Niigata University, Japan
feature list: operation_0337
feature list: operation 3431
feature list: operation 3435
feature list: operation 3891

LOBSTER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0091
application sub category: topic_0769
application sub category: topic 3382
citation: BTZ945
citation: pubmed:31860062
description: An environment to design bioimage analysis workflows for large and complex fluorescence microscopy data. SUMMARY:Open source software such as ImageJ and CellProfiler greatly simplified the quantitative analysis of microscopy images but their applicability is limited by the size, dimensionality and complexity of the images under study. In contrast, software optimized for the needs of specific research projects can overcome these limitations, but they may be harder to find, set up and customize to different needs. Overall, the analysis of large, complex, microscopy images is hence still a critical bottleneck for many Life Scientists. We introduce LOBSTER (Little Objects Segmentation & Tracking Environment), an environment designed to help scientists design and customize image analysis workflows to accurately characterize biological objects from a broad range of fluorescence microscopy images, including large images exceeding workstation main memory.
feature list: operation 3443
feature list: operation 3799

LOINC2HPO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic 3325
application sub category: topic 3360
citation: S41746-019-0110-4
citation: pmcid:PMC6527418
citation: pubmed:31119199
description: Annotation tool that recommends candidate Human Phenotype Ontology (HPO) terms to a LOINC (Laboratory Observation Identifier Names and Codes) test based on lexical matching between HPO term definitions and the name of a laboratory test.
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0002-0736-9199

LOMETS2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic_0160
application sub category: topic 3399
citation: GKZ384
citation: pmcid:PMC6602514
citation: pubmed:31081035
description: LOMETS (Local Meta-Threading Server) is meta-threading method for template-based protein structure prediction.
feature list: operation_0267
feature list: operation_0302
feature list: operation_0474
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Yang Zhang

LONI-QC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0593
application sub category: topic 3384
application sub category: topic 3444
citation: FNINF.2019.00060
citation: pmcid:PMC6722229
citation: pubmed:31555116
description: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data | LONI Quality Control (LONI QC) is an imaging data review and assessment platform for human neuroimaging research studies involving one or more centers. LONI QC allows users to anonymously download imaging data from the LONI IDA and run a standardized quality control check via an automated pre-processing system specifically designed to generate a range of vector statistics and derived images
feature list: operation 3180
feature list: operation 3218
feature list: operation 3431

LOTUS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3474
citation: JOURNAL.PCBI.1007381
citation: pmcid:PMC6786659
citation: pubmed:31568528
description: A single- and multitask machine learning algorithm for the prediction of cancer driver genes. LOTUS is an algorithm for cancer driver gene prediction. This page provides in particular codes to reproduce simulation results. We propose a new computational method called LOTUS to predict new driver genes. LOTUS is a machine-learning based approach which allows to integrate various types of data in a versatile manner, including information about gene mutations and protein-protein interactions. In addition, LOTUS can predict cancer driver genes in a pan-cancer setting as well as for specific cancer types, using a multitask learning strategy to share information across cancer types
feature list: operation 2454
feature list: operation 3436
feature list: operation 3439

LP-SDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 2840
application sub category: topic 3063
application sub category: topic 3378
application sub category: topic 3379
citation: S12911-019-0999-1
citation: pmcid:PMC6918608
citation: pubmed:31849321
description: Combining pre-clinical drug structures and post-market safety reports. Code and Datasets for paper "Towards early detection of adverse drug reactions: combining pre-clinical drug structures and post-market safety reports". This repository contains source code for paper "Towards early detection of adverse drugreactions: combining pre-clinical drug structuresand post-market safety reports" (accepted by BMC Medical Informatics andDecision Making). Please kindly cite the paper if you use the code, datasets or any results in this repo or in the paper:.
feature list: operation 3435
feature list: operation 3907

LPM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic_0659
application sub category: topic 2269
application sub category: topic 2885
application sub category: topic 3517
citation: BTZ947
citation: pubmed:31860024
description: A latent probit model to characterize the relationship among complex traits using summary statistics from multiple GWASs and functional annotations. LPM (Latent Probit Model), is an efficient statistical approach to characterize relationship among complex traits using summary statistics from multiple GWASs and functional annotations. 'LPM' package provides model parameter estimation as well as statistical inference
feature list: operation_0282
feature list: operation 3196
feature list: operation 3557
feature list: operation 3658
feature list: operation 3659

LRCstats
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Script
application sub category: topic_0102
application sub category: topic_0196
citation: btx489
citation: pubmed:29036421
description: Tool for evaluating Long Reads Correction methods.
feature list: operation 3195
feature list: operation 3198
feature list: operation 3219
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md

LRScaf
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0780
application sub category: topic 3168
citation: S12864-019-6337-2
citation: pmcid:PMC6902338
citation: pubmed:31818249
description: Improving draft genomes using long noisy reads. Hybrid assembly strategy is a reasonable and promising approach to utilize strengths and settle weaknesses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologies. According to this principle, we here present a new toolkit named LRScaf (Long Reads Scaffolder) by applied TGS data to improve draft genome assembly. The main features are: short running time, accuracy, and being contiguity. To scaffold rice genome, it could be done in 20 mins with minimap mapper. In human, LRScaf could improve the draft assembly NG50 from 127.5 Kb to 10.4 Mb on 20x PacBio CHM1 dataset and NG50 from 115.7 Kb to 17.4 Mb on ~35x Nanopore NA12878 dataset
feature list: operation_0524
feature list: operation_0525
feature list: operation 3216

LRTK-SIM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3168
application sub category: topic 3174
application sub category: topic 3318
citation: GIZ141
citation: pmcid:PMC6879002
citation: pubmed:31769805
description: Assessment of human diploid genome assembly with 10x Linked-Reads data. A program to simulate linked reads sequencing from 10X Chromium System. LRTK-SIM: Linked read simulator for 10X Chromium System. line2 and line3: Path_Fastahap1 and Path_Fastahap2, the two haploid reference serquences. LRTK-SIM allows one or two fasta files to perform haploid and diploid simulation. The diploid reference sequences can be generated by gen_fasta.py that inserting variants to the reference genome (only SNVs for this version). You can remove Path_Fastahap2=XXX in line3 and set Hap=1 in line33 for haploid simulation.
feature list: operation_0487
feature list: operation_0524
feature list: operation_0525
feature list: operation 3211
feature list: operation 3216
license: MIT

LST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0593
application sub category: topic 3384
application sub category: topic 3444
citation: j.neuroimage.2011.11.032
citation: pubmed:22119648
description: Lesion Segmentation Tool (LST) is an open source toolbox for SPM that is able to segment T2 hyperintense lesions in FLAIR images. Originally developed for the segmentation of MS lesions it has has also been proven to be useful for the segmentation of brain lesions in the context of other diseases, such as diabetes mellitus or Alzheimer's disease.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: LST documentation.pdf
primary contact: Mark Mühlau

LSTD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3382
application sub category: topic 3474
citation: TIP.2019.2938680
citation: pubmed:31502974
description: Progressive Object Transfer Detection | LSTD: A Low-Shot Transfer Detector for Object Detection | Specifically, SSD acts as the region proposal network (RPN) in LSTD. Additionally, we propose Transfer Knowledge (TK) and Background Depression (BD) modules for transfer detection task. More details can be found in LSTD

LSTM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3512
citation: TCBB.2019.2936186
citation: pubmed:31443043
description: Predicting microRNA sequence using CNN and LSTM stacked in Seq2Seq architecture | sequence-prediction-using-CNN-and-LSTMs | microRNA sequence prediction using CNN and LSTM
feature list: operation_0303
feature list: operation_0463

LSTrAP-Lite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: J.BBAGRM.2019.194429
citation: pubmed:31634636
description: Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer. Large-Scale Transcriptome Analysis Pipeline-Lite on credit card-sized ARM computer. If you use LSTrAP-Lite in your research, please cite: Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer. Tan and Mutwil, 2019. (https://doi.org/10.1101/661058).
feature list: operation 1781
feature list: operation 2495
feature list: operation 3439
license: MIT

LSX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0194
application sub category: topic 3293
application sub category: topic 3500
citation: S12859-019-3020-1
citation: pmcid:PMC6693147
citation: pubmed:31409290
description: Automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference | A script in R to run the LS³ and LS⁴ phylogenetic data subsampling algorithms for reducing lineage rate heterogeneity | LSX is a script in R that runs the LS³ and LS⁴ algorithms of data subsampling for multigene phylogenetic inference
license: GPL-3.0

LTER-MARECHIARA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0610
description: Webpage dedicated to the visualization and management of environmental and planktonic data collected at the LTER-MC station in the Gulf of Naples.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

LTMG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: GKZ655
citation: pmcid:PMC6765121
citation: pubmed:31372654
description: A novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data | This repository contains the R codes which could reproduce the results of "LTMG: A statistical model of transcriptional regulatory states in single cell RNA-Seq data" by Changlin Wan, Wennan Chang, Yu Zhang, Fenil Shah, Sha Cao, Melissa L. Fishel, Qin Ma, and Chi Zhang
feature list: operation_0441
feature list: operation 2495
feature list: operation 3223

LUAD LUSC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0749
application sub category: topic 2640
application sub category: topic 3170
citation: S12885-019-5965-X
citation: pmcid:PMC6702745
citation: pubmed:31429720
description: Scripts and Data associated with our publication on genomic signatures to discriminate LUAD and LUSC lung cancer types using TCGA data | Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark | Repository associated to the publication: | Different molecular signatures in lung cancer types from integrative bioinformatic analyses of RNASeq data Marta Lucchetta, Isabelle da Piedade, Mohamed Mounir, Marina Vabistsevits, Thilde Terkelsen, Elena Papaleo*, bioRxiv, doi: https://doi.org/10.1101/501569
feature list: operation 3223
feature list: operation 3463
feature list: operation 3766
license: GPL-3.0

LUCIDus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 3172
application sub category: topic 3360
citation: btz667
citation: pmcid:PMC7986585
citation: pubmed:31504184
description: A Latent Unknown Clustering Integrating Multi-Omics Data (LUCID) with Phenotypic Traits | Latent Unknown Clustering with Integrated Data | An implementation for the 'LUCID' method to jointly estimate latent unknown clusters/subgroups with integrated data. An EM algorithm is used to obtain the latent cluster assignment and model parameter estimates. Feature selection is achieved by applying the regularization method
feature list: operation 3432
license: GPL-2.0

LULU
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3050
application sub category: topic 3168
application sub category: topic 3174
citation: https://doi.org/10.1101/717355
description: A flexible pipeline combining bioinformatic correction tools for prokaryotic and eukaryotic metabarcoding | r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding) | The purpose of LULU is to reduce the number of erroneous OTUs in OTU tables to achieve more realistic biodiversity metrics. By evaluating the co-occurence patterns of OTUs among samples LULU identifies OTUs that consistently satisfy some user selected criteria for being errors of more abundant OTUs and merges these. It has been shown that curation with LULU consistently result in more realistic diversity metrics. The required input of LULU is an OTU table and a corresponding matchlist with all the internal matches of OTUs | A r-package for distribution based post clustering curation of amplicon data
feature list: operation 3192
feature list: operation 3200
feature list: operation 3797
license: LGPL-3.0

LURE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 2640
citation: https://doi.org/10.1101/727891
description: Using Transcriptional Signatures to Find Cancer Drivers with LURE | LURE (Learning UnRealized Events)
feature list: operation 3501

LaMMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3489
citation: PEERJ.PREPRINTS.2247V3
description: The open data geoportal of the Lamma Consortium. In questa categoria sono immagazzinati i dati relativi a bollettini,... In attuazione del decreto legge D. Lgs n. 33 del 14 marzo 2013, che sancisce...

La isla de tomato
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 3810
citation: PP.19.00700
citation: pubmed:31653717
description: Diverse traits contribute to salinity tolerance of wild tomato seedlings from the Galapagos Islands. Analyzing natural variation in Galapagos tomatoes. La_isla_de_tomato App user guide. The manuscript is currently undergoing submission / revision, but this App is available to explore the data freely. The App can be accessed here or run locally from your machine, by typing the following: library("shiny") shiny::runGitHub("mmjulkowska/La_isla_de_tomato", "mmjulkowska").
feature list: operation 2940
feature list: operation 3196
feature list: operation 3432
license: Apache-2.0

LanceletDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: BAZ056
citation: pmcid:PMC6526094
citation: pubmed:31106360
description: Integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species.
feature list: operation 2421
feature list: operation 3431
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Anlong Xu

LandScape
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic 2640
citation: https://doi.org/10.1101/866087
description: A web application for interactive genomic summary visualization. Download and Check the official demo input. Additional demo files from the References are provided in the GitHub project. The 'LandScape' visualization is frequently utilized to provide a systematic illustration of integrative data from multiple layers of batch samples, which are always compared to each other on certain attributes, such as genes and biological pathways mutated in cancers. This online 'LandScape' visualization is designed as a fixed part (histogram and gene-panels) with additional panels (e.g., age, gender, and histology). To visualize data, upload a CSV file in the required format and use sidebar options to customize the display
feature list: operation_0279
feature list: operation_0337
feature list: operation 3802

Laniakea
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
additional type: Workbench
author: https://orcid.org/0000-0002-7088-1283
author: https://orcid.org/0000-0003-3923-2266
citation: giaa033
citation: s12859-021-04401-3
citation: pmcid:PMC7136032
citation: pmcid:PMC8574934
citation: pubmed:32252069
citation: pubmed:34749633
contributor: https://orcid.org/0000-0002-0628-1080
contributor: https://orcid.org/0000-0002-2641-9403
contributor: https://orcid.org/0000-0003-3663-0859
contributor: https://orcid.org/0000-0003-3983-4961
description: Laniakea is a complete software solution to set up a “Galaxy on-demand” Platform as a Service (PaaS). Building on the INDIGO-DataCloud software stack, Laniakea can be deployed over common cloud architectures usually supported both by public and private e-infrastructures. The user interacts with a Laniakea-based service through a simple front-end that allows a general setup of a Galaxy instance, then Laniakea takes care of the automatic deployment of the virtual hardware and the software components. At the end of the process, the user gains access with full administrative privileges to a private, production-grade, fully customisable, Galaxy virtual instance, and to the underlying virtual machine (VM).
license: GPL-3.0
provider: ELIXIR-ITA-INFN
software help: latest
software version: 2.0.0
primary contact: https://orcid.org/0000-0003-3487-4331

LassoNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3474
citation: TVCG.2019.2934332
citation: pubmed:31425100
description: Deep Lasso-Selection of 3D Point Clouds | Zhutian Chen, Wei Zeng, Zhiguang Yang, Lingyun Yu, Chi-Wing Fu, and Huamin Qu IEEE VIS 2019 | Selection is a fundamental task in exploratory analysis and visualization of 3D point clouds

LeGOO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0602
application sub category: topic_0780
application sub category: topic 3172
application sub category: topic 3308
citation: PCZ177
citation: pubmed:31605615
description: An Expertized Knowledge Database for the Model Legume Medicago truncatula. Medicago truncatula was proposed, about three decades ago, as a model legume to study the Rhizobium-legume symbiosis. It has now been adopted to study a wide range of biological questions, including various developmental processes (in particular root, symbiotic nodule and seed development), symbiotic (nitrogen-fixing and arbuscular mycorrhizal endosymbioses) and pathogenic interactions, as well as responses to abiotic stress. With a number of tools and resources set up in M. truncatula for omics, genetics and reverse genetics approaches, massive amounts of data have been produced, as well as four genome sequence releases. Many of these data were generated with heterogeneous tools, notably for transcriptomics studies, and are consequently difficult to integrate
feature list: operation 2421
feature list: operation 2422
feature list: operation 3625

Lead-DBS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3334
application sub category: topic 3384
application sub category: topic 3444
citation: j.neuroimage.2018.08.068
citation: pmcid:PMC6286150
citation: pubmed:30179717
description: MATLAB-toolbox facilitating deep brain stimulation electrode locations and connectomic imaging.
feature list: operation 3435
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 2

Leaf
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3063
application sub category: topic 3303
application sub category: topic 3337
citation: https://doi.org/10.1101/632471
description: Open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research.
feature list: operation_0224
feature list: operation 3478
is accessible for free: true
license: MPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: wiki
primary contact: Sean D. Mooney

LecoS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic_0610
application sub category: topic 2269
citation: PEERJ.PREPRINTS.116V2
description: A QGIS plugin for automated landscape ecology analysis.
feature list: operation 3799

Legofit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic 3056
citation: S12859-019-3154-1
citation: pmcid:PMC6819480
citation: pubmed:31660852
description: Estimating population history from genetic data. Estimate population history parameters from site pattern frequencies. Legofit is a computer package that uses counts of nucleotide site patterns to estimate the history of population size, subdivision, and gene flow.
feature list: operation 2426
feature list: operation 3659

LegumeMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: Multi-organism mine integrates data from legume species: string bean, soybean, peanut and barrel medic
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 11

LeishInDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0091
citation: j.actatropica.2018.12.022
citation: pubmed:30552881
description: Leishmania Inhibitor Database
feature list: operation_0004
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: https://orcid.org/0000-0001-5145-0384

LiGIoNs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0160
application sub category: topic_0820
application sub category: topic 3474
citation: https://doi.org/10.1101/833350
description: A Computational Method for the Detection and Classification of Ligand-Gated Ion Channels. LiGIoNs: Prediction of Ligand Gated Ion Channels. LiGIoNs is a profile Hidden Markov Model based method capable of predicting Ligand-Gated Ion Channels utilizing their special topological information. The method consists of a library of 35 pHMMs, built from the alignment of transmembrane segments of representative LGIC sequences. In addition, 14 Pfam pHMMs are used to further annotate and correctly classify unknown protein sequences into one of the 10 LGIC subfamilies
feature list: operation_0269
feature list: operation_0418
feature list: operation 2241

LiPLike
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3474
citation: https://doi.org/10.1101/651596
description: Towards gene regulatory network predictions of high-certainty | Abstract Motivation Reverse engineering of gene regulatory networks has for years struggled with high correlation in expression between regulatory elements. If two regulators have matching expression patterns it is impossible to differentiate between the two, and thus false positive identifications are abundant. Results To allow for gene regulation predictions of high confidence, we propose a novel method, LiPLike, that assumes a regression model and iteratively searches for interactions that cannot be replaced by a linear combination of other predictors. To compare the performance of LiPLike with other available inference methods, we benchmarked LiPLike using three independent datasets from the previous DREAM5 challenge
feature list: operation_0277
feature list: operation 1781
feature list: operation 3439
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Mika Gustafsson
primary contact: Rasmus Magnusson

Libra
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3050
application sub category: topic 3174
application sub category: topic 3837
citation: giy165
citation: pmcid:PMC6354030
citation: pubmed:30597002
description: Scalable k-mer-based tool for massive all-vs-all metagenome comparisons.
feature list: operation_0310
feature list: operation 2495
feature list: operation 3472
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Illyoung Choi

LiceBase
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
  encoding format: format 2330
  encoding format: format 2331
  encoding format: format 3752
input: Experimental measurement
  type: FormalParameter
  additional type: data 3108
  encoding format: format 2331
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2330
input: Gene name
  type: FormalParameter
  additional type: data 2299
  encoding format: format 2330
input: Tool name (BLAST)
  type: FormalParameter
  additional type: data 1192
  encoding format: format 2331
input: Morphology parameter
  type: FormalParameter
  additional type: data 3723
  encoding format: format 2330
input: Phenotype name
  type: FormalParameter
  additional type: data 3275
  encoding format: format 2331
input: Taxon
  type: FormalParameter
  additional type: data 1868
  encoding format: format 2331
input: Species name
  type: FormalParameter
  additional type: data 1045
  encoding format: format 2331
input: Database ID
  type: FormalParameter
  additional type: data 1048
  encoding format: format 2331
input: Sequence
  type: FormalParameter
  additional type: data 2044
  encoding format: format 1929
  encoding format: format 1935
  encoding format: format 2330
  encoding format: format 2571
input: Species name
  type: FormalParameter
  additional type: data 1045
  encoding format: format 2331
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2330
output: Sequence search results
  type: FormalParameter
  additional type: data_0857
  encoding format: format 1333
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2331
output: Sequence set
  type: FormalParameter
  additional type: data_0850
  encoding format: format 1929
output: Sequence report
  type: FormalParameter
  additional type: data 2955
  encoding format: format 1333
  encoding format: format 2330
  encoding format: format 2331
  encoding format: format 3547
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0091
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic 3071
application sub category: topic 3302
application sub category: topic 3387
application sub category: topic 3810
author: https://orcid.org/0000-0002-2371-5928
author: Sea Lice Research Centre (SLRC)
author: Wei Zhang
description: LiceBase is a genomics database for sea lice (Lepeophtheirus salmonis and Caligus spp.), which are major pathogens affecting the global salmon farming industry. The database contains the genome annotation of the Atlantic salmon louse (L. salmonis) and is designed to help researchers, industry professionals, and other interested parties access and share information about these parasites, with the goal of developing new treatment methods and tools to ensure a sustainable salmon farming industry. LiceBase provides annotated genome reports, genome browsing, RNA interference (RNAi) experiment browsing for several additional species, BLAST search, and in-situ images. The database homepage posts news updates and recent publications related to sea lice and salmonid species.
feature list: operation_0305
feature list: operation_0346
feature list: operation 2421
feature list: operation 2422
feature list: operation 3208
funder: The Research Council of Norway
is accessible for free: true
license: CC-BY-SA-4.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: University of Bergen
software help: https://licebase.org/
software help: about
software help: privacy policy
software help: terms of use
primary contact: https://orcid.org/0000-0002-2371-5928
primary contact: https://orcid.org/0000-0003-4110-0748

Lifemap
type: SoftwareApplication
input: Taxonomy
  type: FormalParameter
  additional type: data 3028
output: Taxonomy
  type: FormalParameter
  additional type: data 3028
  encoding format: format 1910
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic 3050
application sub category: topic 3299
citation: journal.pbio
description: Explorer of the entire tree of life. Lifemap allows visualizing the entire NCBI taxonomy on a single page with a deep zoom interface and performing easy search, mrca detection, subtree download, etc.
feature list: operation_0337
feature list: operation_0567
feature list: operation 2421
feature list: operation 2422
is accessible for free: true
license: CC-BY-NC-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
software version: 1.0

LightCpG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3673
citation: S12864-019-5742-X
citation: pmcid:PMC6513517
citation: pubmed:31084602
description: Multi-view CpG sites detection on single-cell whole genome sequence data.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0001-8346-0798

LikeLTD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic_0654
citation: sagmb-2016-0038
citation: pubmed:27416618
description: Tool to determine DNA profile weight of evidence.
feature list: operation 2937
feature list: operation 3196
feature list: operation 3629
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: likeLTD.pdf
software help: usage.pdf
software version: 6.3.0
primary contact: Christopher Steele

Lilikoi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3172
citation: giy136
citation: pmcid:PMC6290884
citation: pubmed:30535020
description: R package for personalized pathway-based classification modeling using metabolomics data.
feature list: operation_0533
feature list: operation 3501
feature list: operation 3659
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: lilikoi.pdf
primary contact: Fadhl Alakwaa

LinX
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
  encoding format: format 2330
input: Reaction data
  type: FormalParameter
  additional type: data 2978
  encoding format: format 2330
output: Data
  type: FormalParameter
  additional type: data_0006
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0077
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0601
application sub category: topic 3314
application sub category: topic 3520
citation: ACS.JPROTEOME.0C00858
citation: pubmed:33657806
description: LinX is a Java language-based program designed for fast assignment, evaluation, and validation of mass spectrometric datasets from chemical cross-linking.
feature list: operation_0389
feature list: operation 2945
feature list: operation 3767
feature list: operation 3860
is accessible for free: true
license: Not licensed
operating system: Windows
software help: downloads.php
software version: 1.1
primary contact: 0000-0001-7569-843X

Linclust
type: SoftwareApplication
input: Sequence set
  type: FormalParameter
  additional type: data_0850
  encoding format: format 2182
  encoding format: format 2200
output: Sequence cluster
  type: FormalParameter
  additional type: data 1235
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0077
application sub category: topic_0078
application sub category: topic_0080
application sub category: topic_0623
application sub category: topic 3174
citation: s41467-018-04964-5
citation: pmcid:PMC6026198
citation: pubmed:29959318
description: Linclust is the first clustering algorithm whose runtime scales linearly. With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity.
feature list: operation_0291
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: metaG-ECCB18-partII
software help: wiki
primary contact: Söding Lab

LinearFold
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic 3512
application sub category: topic 3542
citation: BTZ375
citation: pmcid:PMC6681470
citation: pubmed:31510672
description: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search | The new source code of the LinearFold, linear-time prediction for RNA secondary structures | This codebase replaces the now deprecated version: https://github.com/abentu0101/LinearFold. This version fixes many bugs and design problems in the old version | Add a sequence Paste or type your sequence here (length < 100,000): | GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGG | Choose model(s) LinearFold-C (using CONTRAfold v2.0 machine-learned model, Do et al 2006) | * Liang Huang, **He Zhang, **Dezhong Deng, Kai Zhao, Kaibo Liu, David Hendrix, and David H. Mathews (2019). LinearFold: Linear-Time Approximate RNA Folding by 5’-to-3’ Dynamic Programming and Beam Search. Bioinformatics, Volume 35, Issue 14, July 2019, Pages i295–i304. ISMB 2019
feature list: operation_0278
feature list: operation_0481
feature list: operation 1812

Link-HD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0091
application sub category: topic_0780
citation: btz862
citation: pmcid:PMC7141858
citation: pubmed:31738392
description: a versatile framework to explore and integrate heterogeneous microbial communities. a versatile approach to integrate heterogeneous datasets. LinkHD: a versatile framework to explore and integrate heterogeneous data. Here we present Link-HD, an approach to integrate heterogeneous datasets, as a generalization of STATIS-ACT (“Structuration des Tableaux A Trois Indices de la Statistique Analyse Conjointe de Tableaux”), a family of methods to join and compare information from multiple subspaces. Laura Zingaretti & Yuliaxis Ramayo Caldas. Laura M Zingaretti, Gilles Renand, Diego P Morgavi, Yuliaxis Ramayo-Caldas, Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities, Bioinformatics, https://doi.org/10.1093/bioinformatics/btz862
feature list: operation 3501
feature list: operation 3659
license: GPL-3.0

LinkPhinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0601
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3474
citation: https://doi.org/10.1101/865055
description: Accurate Prediction of Kinase-Substrate Networks Using Knowledge Graphs. Abstract Phosphorylation of specific substrates by protein kinases is a key control mechanism for vital cell-fate decisions and other cellular processes. However, discovering specific kinase-substrate relationships is timeconsuming and often rather serendipitous. Computational predictions alleviate these challenges, but the current approaches suffer from limitations like restricted kinome coverage and inaccuracy. They also typically utilise only local features without reflecting broader interaction context. To address these limitations, we have developed an alternative predictive model.
feature list: operation_0269
feature list: operation_0417
feature list: operation 3439

LinkeDomics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 2830
citation: MD.0000000000015774
citation: pmcid:PMC6571408
citation: pubmed:31124967
description: Publicly available portal that includes multi-omics data from all 32 TCGA Cancer types. It also includes mass spectrometry-based proteomics data generated by the Clinical Proteomics Tumor Analysis Consortium (CPTAC) for TCGA breast, colorectal and ovarian tumors.
feature list: operation 2436
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: LinkedOmicsManual 1.1.pdf
software help: LinkedOmics Workshop 10042017.pdf
primary contact: Xiaohua Chen

Linked Registries
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic 3325
citation: https://doi.org/10.1155/2017/8327980
citation: pmcid:PMC5682045
citation: pubmed:29214177
description: Connects rare diseases patient registries through a Semantic Web Layer.
feature list: operation 2422
feature list: operation 3283
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

LipMat
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0121
application sub category: topic_0153
application sub category: topic_0593
application sub category: topic 3172
application sub category: topic 3520
citation: ACSOMEGA.9B03463
citation: pmcid:PMC6921604
citation: pubmed:31867556
description: Fast and Quantitative Phospholipidomic Analysis of SH-SY5Y Neuroblastoma Cell Cultures Using Liquid Chromatography-Tandem Mass Spectrometry and 31P Nuclear Magnetic Resonance. Matlab Script for automated LC-MS/MS phospholipid analysis. LipMat script is a set of tools for automated LC-MS/MS phospholipid analysis. Paper is in preparation and this section will be updated when it will be published. Matlab Script for automated LC-MS/MS lipid analysis.
feature list: operation 3215
feature list: operation 3799
feature list: operation 3860
license: GPL-3.0

Lipase Engineering Database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic_0736
citation: FEBS.15071
citation: pubmed:31545554
description: The modular structure of α/β-hydrolases | The BioCatNet Database System aims to collect and present comprehensive information about biocatalysators: sequence, structure, educts, products, environmental conditions and kinetics | The Lipase Engineering Database (LED) version4.0.0 | Widmann M., Juhl PB. & Pleiss J. (2010). Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A. BMC Genomics 11: 123
feature list: operation_0303
feature list: operation 3431
feature list: operation 3798

Lipase reclassification
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0623
application sub category: topic_0821
application sub category: topic 3534
citation: PEERJ.PREPRINTS.27725
description: Deposit and classification of lipolytic enzymes based on the proposed classification system in Hitch and Clavel (TBP).
feature list: operation_0483
feature list: operation 3431
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Thomas C. A. Hitch

LipidIMMS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0153
application sub category: topic_0769
application sub category: topic 3314
application sub category: topic 3407
citation: 978-1-0716-0030-6 17
citation: pubmed:31729667
description: The Use of LipidIMMS Analyzer for Lipid Identification in Ion Mobility-Mass Spectrometry-Based Untargeted Lipidomics. Questions: zhouzw AT sioc.ac.cn, jiangzhu AT sioc.ac.cn. © Zhu lab , Interdisciplinary Research Center on Biology and Chemistry (IRCBC), Chinese Academy of Sciences (CAS). All Rights Reserved.
feature list: operation 3215
feature list: operation 3629
feature list: operation 3860

LipidMS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0153
application sub category: topic 3337
application sub category: topic 3520
citation: acs.analchem.8b03409
citation: pubmed:30500173
description: R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics.
feature list: operation 3629
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0
primary contact: M Isabel Alcoriza-Balaguer

LipidMatch Normalizer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0153
application sub category: topic_0769
application sub category: topic 3520
citation: s12859-019-2803-8
citation: pmcid:PMC6489209
citation: pubmed:31035918
description: Software tool for internal standard based normalization of lipids, and effect of data-processing strategies on resulting values.
feature list: operation 3629
feature list: operation 3633
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://github.com/GarrettLab-UF/LipidMatch-Normalizer/blob/master/2018_07_19_LMN_Instructions.docx
software version: 1.0.2
primary contact: Jason Cochran
primary contact: Jeremy Koelmel

Lipid Mini-On
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0089
application sub category: topic_0153
citation: btz250
description: Lipid Mining and Ontology (Lipid Mini-On) - mining and ontology tool for enrichment analysis of lipidomic data.
feature list: operation 3501
feature list: operation 3798
is accessible for free: true
license: BSD-2-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: lipid-mini-on
primary contact: Geremy Clair
primary contact: Jennifer E. Kyle

LnCeVar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0199
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3068
citation: gkz887
citation: pmcid:PMC7145649
citation: pubmed:31617563
description: A comprehensive database of genomic variations that disturb ceRNA network regulation. Genomic VA,T,C,G RIATION disturbing ceRNA regulations. LnCeVar is a comprehensive database that aims to infer genomic variations that disturb lncRNA-associated ceRNA regulation. e.g. NEAT1, TP53, hsa-let-7b-5p, rs3825071, COSN13341324, BRCA
feature list: operation 2421
feature list: operation 3196
feature list: operation 3208
feature list: operation 3503
feature list: operation 3659

LncADeep
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 3068
citation: bty428
citation: pubmed:29850816
description: ab initio lncRNA identification and functional annotation tool based on deep learning.
feature list: operation_0476
feature list: operation 2495
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: lncadeep
primary contact: Huaiqiu Zhu

LncBook
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0097
application sub category: topic_0634
application sub category: topic_0659
citation: cpbi.82
citation: pubmed:31524988
description: LncBook accommodates a high-quality collection of human lncRNA genes and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional signatures of lncRNAs in human diseases and different biological contexts.
feature list: operation_0314
feature list: operation_0417
feature list: operation 2495
feature list: operation 3792
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 2.0

LncTarD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3295
application sub category: topic 3360
citation: gkz985
citation: pmcid:PMC7145524
citation: pubmed:31713618
description: A manually-curated database of experimentally-supported functional lncRNA-target regulations in human diseases. Search and download the information for the Mutual exclusivity. MutExGenome is a database of Mutual Exclusive mutations in mutiple species. LncTarD provides key lncRNA-target regulations, their influenced functions and lncRNA-mediated regulatory mechanisms in human diseases. Quick Search, start typing keywords, press ESC to close suggestions
feature list: operation 2421
feature list: operation 3439
feature list: operation 3446

LncVar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 2885
citation: 978-1-4939-8808-2 14
citation: btw581
citation: pubmed:27605101
citation: pubmed:30539556
description: Database of genetic variations associated with long noncoding genes.
feature list: operation_0484
feature list: operation 3196
feature list: operation 3232
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: faqs.php

LoReAn
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3512
citation: pp.18.00848
citation: pubmed:30401722
description: Automated eukaryotic genome annotation based on long-read cDNA sequencing.
feature list: operation_0308
feature list: operation_0362
feature list: operation_0476
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: INSTALL.md
primary contact: Luigi Faino

LocPL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic_0140
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 2229
citation: S12859-019-3077-X
citation: pmcid:PMC6886211
citation: pubmed:31787091
description: Integrating protein localization with automated signaling pathway reconstruction. Are you sure you want to delete this graph?
feature list: operation_0277
feature list: operation 3083
feature list: operation 3439

LocustMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: An integrated Omics data warehouse for Locust, Locusta migratoria
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 1.2

Logomaker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3068
application sub category: topic 3512
application sub category: topic 3855
citation: https://doi.org/10.1101/635029
description: Beautiful sequence logos in python | Software for the visualization of sequence-function relationships | beautiful sequence logos in Python — logomaker 0.8 documentation | Logomaker can be installed from PyPI by executing | Software for creating highly customized sequence logos | Free document hosting provided by Read the Docs
feature list: operation_0337
feature list: operation 3501
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: logomaker.readthedocs.io
primary contact: Ammar Tareen
primary contact: Justin Kinney

Look4TRs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0160
application sub category: topic 2885
citation: btz551
citation: pubmed:31287494
description: de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models.
feature list: operation 3359
feature list: operation 3472
feature list: operation 3798
is accessible for free: true
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Hani Z. Girgis

Loxodonta Localizer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0632
application sub category: topic 2885
application sub category: topic 3068
application sub category: topic 3168
citation: ESZ058
citation: pubmed:31674643
description: A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA. git clone https://github.com/kaizhao86/loxodontalocalizer. Loxodonta Localizer maps the localities from which mitochondrial DNA sequences have been reported for African elephants, Loxodonta africana and L. cyclotis, using the dataset described in Ishida et al., 2013, updated with additional sequences. #first, install Python 2.7, pip and git
feature list: operation_0224
feature list: operation_0487
feature list: operation 3192

LungMAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0121
application sub category: topic 3067
application sub category: topic 3172
application sub category: topic 3382
citation: S13326-019-0209-1
citation: pmcid:PMC6814058
citation: pubmed:31651362
description: A comparison of alveolar formation and maturation within mouse and human lung. Anatomic Ontology for Mouse Lung Maturation. Cell Ontology for Mouse Lung Maturation. Anatomic Ontology for Human Lung Maturation. Cell Ontology for Human Lung Maturation. Search BREATH to explore the developing lung. LungMAP provides users with a tool to annotate images within the website. This webpage provides instructions on how to annotate an image using the tool. Image annotation to convey specific information about an image, importantly, in the context of the image increases its value exponentially, especially with resolution on the molecular level. LungMAP human and mouse ontologies reference page provides links to the LungMAP Ontology Browser, Release Notes, and text files for the scientific community to view the ontologies.
feature list: operation 2422
feature list: operation 2495
feature list: operation 3352
feature list: operation 3553

LupinMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: White and narrow-leaf lupin data from the Legume Information System
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 2

LutzoDexTM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0621
application sub category: topic 3382
application sub category: topic 3500
citation: ZOOTAXA.4688.3.4
citation: pubmed:31719438
description: Digital key for Brazilian sand flies (Diptera, Phlebotominae) within an Android App. Here we present an Android mobile application (app) for the identification of Brazilian phlebotomine sand fly species. The app, which is named LutzoDex™, relies on information included in a data source with morphological and morphometrical characters. This tool can present up to seven answer options to a question. Images of morphological structures can be referenced to make identification easier, and users can see a list of possible species based on the features they report. Maps are also used to determine the geographical distribution and whether the species is incriminated or suspected as a vector of Leishmania spp. in Brazil. The app is available free of charge in both English and Portuguese in the Google Play Store at https: play.google.com store apps details?id=max.com.lutzodexhl=pt_BR.

LuxR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3170
application sub category: topic 3179
application sub category: topic 3519
citation: GKZ1089
citation: pubmed:31745565
description: Global H-NS counter-silencing by LuxR activates quorum sensing gene expression. FileUtil.pm - perl helper module for loading files reformatFasta.pl - perl script the cleans and reformats multi-fasta files findOverlaps.pl - perl script to identify sets of overlapping peaks for Venn diagram getPeakAnno.pl - perl script to add annotation information to Macs2 peaks getGenePeakAnno2.pl - perl script to add peaks to gene information findClosest2.pl - perl script to produce table relating luxR peaks to H-NS double peaks.
feature list: operation_0308
feature list: operation_0335
feature list: operation_0435
feature list: operation_0440
feature list: operation 3222

LyoPRONTO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3068
citation: S12249-019-1532-7
citation: pmcid:PMC6823652
citation: pubmed:31673810
description: An Open-Source Lyophilization Process Optimization Tool. This work presents a new user-friendly lyophilization simulation and process optimization tool, freely available under the name LyoPRONTO. This tool comprises freezing and primary drying calculators, a design-space generator, and a primary drying optimizer. The freezing calculator performs 0D lumped capacitance modeling to predict the product temperature variation with time which shows reasonably good agreement with experimental measurements. The primary drying calculator performs 1D heat and mass transfer analysis in a vial and predicts the drying time with an average deviation of 3% from experiments. The calculator is also extended to generate a design space over a range of chamber pressures and shelf temperatures to predict the most optimal setpoints for operation.
feature list: operation 2426
feature list: operation 3659
feature list: operation 3799

M-GCTA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3295
citation: S10519-019-09969-4
citation: pubmed:31493278
description: Introducing M-GCTA a Software Package to Estimate Maternal (or Paternal) Genetic Effects on Offspring Phenotypes | *This document is under developement. Your ideas and suggestions are always welcome! | M-GCTA is an user-friendly software package, which can be used to estimate the proportion of phenotypic variance due to tagged maternal (or paternal) and offspring genetic effects on offspring phenotypes using large studies where genome-wide genotype data are available on mother- (or father-) offspring pairs
feature list: operation 3196
feature list: operation 3211
feature list: operation 3557

M-TRACK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 2229
application sub category: topic 3295
application sub category: topic 3300
application sub category: topic 3382
citation: https://doi.org/10.1101/2019.12.12.874248
description: A platform for live cell multiplex imaging reveals cell phenotypic transition dynamics inherently missing in snapshot data. M-TRACK is a live cell imaging analysis tool
feature list: operation 3216
feature list: operation 3443
feature list: operation 3891
license: GPL-3.0

M1CR0B1AL1Z3R
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0084
application sub category: topic 3473
application sub category: topic 3697
citation: GKZ423
citation: pmcid:PMC6602433
citation: pubmed:31114912
description: Web server for the analysis of large-scale microbial genomics data.
feature list: operation_0306
feature list: operation 3478
feature list: operation 3745
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: faq.html
primary contact: Tal Pupko

M3S
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0099
application sub category: topic 3170
application sub category: topic 3308
citation: S12859-019-3243-1
citation: pmcid:PMC6923906
citation: pubmed:31861972
description: A comprehensive model selection for multi-modal single-cell RNA sequencing data. M3S: A user-friendly tool for comprehensive evaluation of multi-modality and statistical model selection for single-cell RNA sequencing data. A large number of single-cell RNA sequencing (scRNA-seq) data set was recently generated to characterize the heterogeneous in cell types or states in a complex tissue or biological process
feature list: operation 2495
feature list: operation 3223
feature list: operation 3664

MAC-INMV-SSR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3489
citation: J.MEEGID.2019.104075
citation: pubmed:31634642
description: A web application dedicated to genotyping members of Mycobacterium avium complex (MAC) including Mycobacterium avium subsp. paratuberculosis strains. Genotyping of Mycobacterium avium subsp. paratuberculosis (Map) is an indispensable tool for surveillance of this significant veterinary pathogen. For Map, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRUs) and other variable number variable-number tandem repeats (VNTRs) was established using 8 markers. In the recent past this standard, portable, reproducible and discriminatory typing method has been frequently applied alone or in combinations with multi-locus short-sequence-repeat (MLSSR) sequencing. With the widespread use of these genotyping methods, standardization between laboratories needs to be managed, and knowledge of existing profiles and newly defined genotypes should be indexed and shared.
feature list: operation 3196

MACV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0176
application sub category: topic_0199
application sub category: topic 3306
citation: peerj.preprints.138v3
description: Analyzing Machupo virus-receptor binding by molecular dynamics simulations. Code and data for Meyer et al, Analyzing Machupo virus-receptor binding by molecular dynamics simulations, PeerJ 2:e266 (2014). This file is meant to explain each of the top level directories. There should be a similar readme in the relevant folders. eq_analysis - contains the scripts used to generate the equilibration rmsf plots as well as the plot themselves. fep_config - contains everything necessary to run the dual topology fep.
feature list: operation_0337
feature list: operation 2476
feature list: operation 2492

MADOKA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0108
application sub category: topic_0154
application sub category: topic 2814
citation: S12859-019-3235-1
citation: pmcid:PMC6929402
citation: pubmed:31870277
description: An ultra-fast approach for large-scale protein structure similarity searching. Protein similarity search in PDB. Ultra-fast and Large-Scale Protein Structural Neighbor Searching. MADOKA, a webserver features on searching similar protein structures by aligning input structure with the whole PDB library implemented by MADOKA, an algorithm for matching protein structures by two phases.
feature list: operation_0360
feature list: operation_0491
feature list: operation_0503
feature list: operation_0510
feature list: operation 3454

MADloy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3518
citation: https://doi.org/10.1101/764845
description: Robust detection of mosaic loss of chromosome Y from genotype-array-intensity data | R package to detect mosaic loss of Y events in SNP array and NGS data | R package to detect mosaic loss of Y events (LOY) from SNP array data
feature list: operation_0484
feature list: operation 3196
feature list: operation 3501

MAFFT
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
  encoding format: format 1929
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0080
citation: 978-1-62703-646-7 8
citation: bbx108
citation: bty121
citation: mst010
citation: gki198
citation: f1000research.1114334.1
citation: pmcid:PMC3603318
citation: pmcid:PMC548345
citation: pmcid:PMC6041967
citation: pmcid:PMC6781576
citation: pubmed:15661851
citation: pubmed:23329690
citation: pubmed:24170399
citation: pubmed:28968734
citation: pubmed:29506019
description: MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.
feature list: operation_0492
is accessible for free: true
license: BSD-Source-Code
operating system: Linux
operating system: Mac
operating system: Windows
software help: tips0.html

MAFFT-DASH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0084
application sub category: topic_0097
application sub category: topic_0154
citation: GKZ342
citation: pmcid:PMC6602451
citation: pubmed:31062021
description: Multiple alignment program for amino acid or nucleotide sequences.
feature list: operation_0503
feature list: operation_0504
feature list: operation_0509
is accessible for free: true
license: GPL-1.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: tips0.html
primary contact: https://orcid.org/0000-0003-4133-8393
primary contact: Daron M. Standley

MAFFT API (EBI)
type: SoftwareApplication
input: Sequence alignment
  type: FormalParameter
  additional type: data_0863
  encoding format: format 1929
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0080
citation: bbn013
citation: pubmed:18372315
description: High speed multiple sequence alignment program.
feature list: operation_0492
operating system: Linux
operating system: Mac
operating system: Windows
software help: mafft rest
software version: 1

MAGI-S
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic_0659
application sub category: topic 3334
citation: S13073-019-0678-Y
citation: pmcid:PMC6815046
citation: pubmed:31653223
description: Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders. Seed-centric method to identify gene modules of similar interaction and co-expression characteristics. Merge A ffected G enes into I ntegrated networks.
feature list: operation 3196
feature list: operation 3439
feature list: operation 3501

MAGO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0084
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3316
application sub category: topic 3697
citation: msz237
citation: pmcid:PMC6993843
citation: pubmed:31633780
description: Computational framework for high-quality production and large-scale evolutionary analysis of metagenome assembled genomes. Microbial species play important roles in different environments and the production of high-quality genomes from metagenome datasets represents a major obstacle to understanding their ecological and evolutionary dynamics. Metagenome-Assembled Genomes Orchestra (MAGO) is a computational framework that integrates and simplifies metagenome assembly, binning, bin improvement, bin quality (completeness and contamination), bin annotation, and evolutionary placement of bins via detailed maximum-likelihood phylogeny based on multiple marker genes using different amino acid substitution models, next to average nucleotide identity analysis of genomes for delineation of species boundaries and operational taxonomic units
feature list: operation_0310
feature list: operation_0362
feature list: operation 3798

MAGOS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0084
application sub category: topic 2640
application sub category: topic 2885
application sub category: topic 3676
citation: https://doi.org/10.1101/790386
description: Discovering Subclones in Tumors Sequenced at Standard Depths. MAGOS: Model-based Adaptive Grouping of Subclones
feature list: operation 3196
feature list: operation 3432
feature list: operation 3435

MAGenTA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Suite
application sub category: topic_0659
application sub category: topic_0798
application sub category: topic 3301
citation: btx320
citation: pmcid:PMC5860071
citation: pubmed:28498899
description: Microbial Assessment by Genome-wide Tn-Seq Analysis (MAGenTA) - Galaxy implemented tool for complete Tn-Seq analysis and data visualization.
feature list: operation 2495
feature list: operation 3192
feature list: operation 3196
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: magentaManual.pdf
primary contact: Tim van Opijnen

MAJIQ-SPEL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web API
additional type: Web service
application sub category: topic_0632
application sub category: topic 3170
application sub category: topic 3320
citation: btx565
citation: pmcid:PMC7263396
citation: pubmed:28968636
description: Web-tool to interrogate classical and complex splicing variations from RNA-Seq data.
feature list: operation_0308
feature list: operation 3237
feature list: operation 3800
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: docs
software version: 0.2
primary contact: Yoseph Barash

MALINI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0634
application sub category: topic 3334
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3474
citation: s11682-019-00191-8
citation: pmcid:PMC7198352
citation: pubmed:31691160
description: Supervised machine learning for diagnostic classification from large-scale neuroimaging datasets. Machine Learning in NeuroImaging (MALINI) is a MATLAB-based toolbox used for feature extraction and disease classification using resting state functional magnetic resonance imaging (rs-fMRI) data. 18 different popular classifiers are presented. With slight modifications, it can also be used for any classification problem using any set of features
feature list: operation 2428
feature list: operation 3283
feature list: operation 3435
license: MIT

MANET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0194
application sub category: topic_0602
application sub category: topic_0736
application sub category: topic_0821
application sub category: topic 3407
citation: JOURNAL.PONE.0224201
citation: pmcid:PMC6812854
citation: pubmed:31648227
description: Hierarchy and modularity in evolving metabolic networks. Enzyme recruitment is a fundamental evolutionary driver of modern metabolism. We see evidence of recruitment at work in the metabolic Molecular Ancestry Networks (MANET) database, an online resource that integrates data from KEGG, SCOP and structural phylogenomic reconstruction. The database, which was introduced in 2006, traces the deep history of the structural domains of enzymes in metabolic pathways. Here we release version 3.0 of MANET, which updates data from KEGG and SCOP, links enzyme and PDB information with PDBsum, and traces evolutionary information of domains defined at fold family level of SCOP classification in metabolic subnetwork diagrams.
feature list: operation_0277
feature list: operation 3083
feature list: operation 3660

MAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0108
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: S41421-019-0107-9
citation: pmcid:PMC6796874
citation: pubmed:31636953
description: Model-based analysis of proteomic data to detect proteins with significant abundance changes. MAP (Model-based Analysis of Proteomic data), is designed to statistically compare the proteomic profiles generated from different biological samples using the isotope labeling based mass spectrometry (MS) technique and directly identify proteins with significant abundance changes. Unlike many existing tools for this purpose, it does not require parallel/additional technical replicates to fathom technical variations; instead, MAP uses a novel step-by-step regression analysis to directly model technical variations from the profiles under comparison. Therefore, experimental designs and their expenses can be simplified and reduced for more practices
feature list: operation 2429
feature list: operation 2495
feature list: operation 3638
feature list: operation 3659

MAPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0102
application sub category: topic 3169
application sub category: topic 3179
citation: journal.pcbi.1006982
citation: pmcid:PMC6483256
citation: pubmed:30986246
description: MAPS (Model-based Analysis of PLAC-Seq data) pipeline is a a set of multiple scripts used to analyze PLAC-Seq and HiChIP data.
feature list: operation 2429
feature list: operation 3222
feature list: operation 3798
is accessible for free: true
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Ivan Juric
primary contact: Ming Hu

MARGO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3382
application sub category: topic 3500
application sub category: topic 3524
citation: JOURNAL.PONE.0224243
citation: pmcid:PMC6876843
citation: pubmed:31765421
description: MARGO (Massively Automated Real-time GUI for Object-tracking). Fast object tracking in real time allows convenient tracking of very large numbers of animals and closed-loop experiments that control stimuli for many animals in parallel. We developed MARGO, a MATLAB-based, real-time animal tracking suite for custom behavioral experiments. We demonstrated that MARGO can rapidly and accurately track large numbers of animals in parallel over very long timescales, typically when spatially separated such as in multiwell plates. We incorporated control of peripheral hardware, and implemented a flexible software architecture for defining new experimental routines. These features enable closed-loop delivery of stimuli to many individuals simultaneously. We highlight MARGO's ability to coordinate tracking and hardware control with two custom behavioral assays (measuring phototaxis and optomotor response) and one optogenetic operant conditioning assay.
feature list: operation 3435
feature list: operation 3450

MARIA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 2830
application sub category: topic 3474
citation: s41587-019-0280-2
citation: pmcid:PMC7075463
citation: pubmed:31611695
description: Predicting HLA class II antigen presentation through integrated deep learning. MARIA is a machine learning tool developed by Chen et al. to predict likelihood of HLA-II peptide ligand presentation given cell HLA alleles, peptide sequences, and source genes of the peptides.
feature list: operation_0252
feature list: operation_0416
feature list: operation 2454
feature list: operation 3439

MARMoSET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic_0634
application sub category: topic 3520
citation: MCP.TIR119.001505
citation: pubmed:31097673
description: Extracting Publication-ready Mass Spectrometry Metadata from RAW Files.
feature list: operation_0335
feature list: operation 2422
feature list: operation 3627
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Johannes Graumann
primary contact: Mario Looso

MARSHAL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 3306
application sub category: topic 3810
citation: https://doi.org/10.1101/798975
description: Novel tool for virtual phenotyping of maize root system hydraulic architectures. How to use MARSHAL from the R environment. install_github("MARSHAL-ROOT/marshal"). MAize Root System Hydraulic Architecture soLver. MARSHAL is a maize root system hydraulic architecture solver that combines the root architecture model CRootBox (Schnepf et al. 2018) with the method for solving water flow in RSHA of Meunier et al. (2017) and with the method for computing macroscopic parameter of Couvreur et al. (2012). To load the package, you can use the command:
feature list: operation 2426
license: Apache-2.0

Mascot Server
type: SoftwareApplication
input: Peptide mass fingerprint
  type: FormalParameter
  additional type: data_0944
  encoding format: format 1915
  encoding format: format 2330
  encoding format: format 3651
  encoding format: format 3834
input: Mass spectrometry spectra
  type: FormalParameter
  additional type: data_0943
  encoding format: format 1915
  encoding format: format 3244
  encoding format: format 3651
  encoding format: format 3652
  encoding format: format 3653
  encoding format: format 3834
output: Peptide identification
  type: FormalParameter
  additional type: data_0945
  encoding format: format 2332
  encoding format: format 3247
  encoding format: format 3651
  encoding format: format 3681
  encoding format: format 3713
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0121
application sub category: topic 3520
citation: mcp.m110.003822
citation: pmcid:PMC3108832
citation: pubmed:10612281
citation: pubmed:12422359
citation: pubmed:21447708
description: The leading software package for protein identification and characterisation using mass spectrometry data.
feature list: operation 2929
feature list: operation 3639
feature list: operation 3641
feature list: operation 3643
feature list: operation 3646
feature list: operation 3647
feature list: operation 3649
feature list: operation 3767
feature list: operation 3801
is accessible for free: false
license: Proprietary
operating system: Linux
operating system: Windows
software help: help.html
primary contact: see publication

MASSIF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0160
application sub category: topic_0736
application sub category: topic 3169
citation: btz855
citation: pmcid:PMC7703792
citation: pubmed:31742324
description: Improved linking of motifs to their TFs using domain information. Improved motif enrichment analysis using protein domain type information. MASSIF - motif association with domain information. MASSIF is a novel method to improve the performance of existing tool that link motifs to TFs relying on TF-associated sequences.
feature list: operation_0238
feature list: operation_0239
feature list: operation_0240
license: MIT

MAtCHap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic_0654
application sub category: topic 3168
citation: https://doi.org/10.1101/860262
description: an ultra fast algorithm for solving the single individual haplotype assembly problem. Abstract Background Human genomes are diploid, which means they have two homologous copies of each chromosome and the assignment of heterozygous variants to each chromosome copy, the haplotype assembly problem, is of fundamental importance for medical and population genetics. While short reads from second generation sequencing platforms drastically limit haplotype reconstruction as the great majority of reads do not allow to link many variants together, novel long reads from third generation sequencing can span several variants along the genome allowing to infer much longer haplotype blocks
feature list: operation_0310
feature list: operation_0487
feature list: operation 3196
feature list: operation 3211

MBITES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0610
application sub category: topic_0621
application sub category: topic 2269
application sub category: topic 3324
citation: https://doi.org/10.1101/790097
description: Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology. bionomics.cpp: fast functions in C++ to calculate summary statistics of interest from simulation output. trivial-simulation.R: run MBITES on a very simple landscape (used for model comparison) and generate plots to compare with MBDETES. bionomics.R: takes output generated by peridomestic-simulation.R and generates output to make figures
feature list: operation 2426
feature list: operation 3659

MBKbase rice
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 2885
application sub category: topic 3673
citation: gkz921
citation: pmcid:PMC7145604
citation: pubmed:31624841
description: An integrated omics knowledgebase for molecular breeding in rice. Rice Phenotype Search and Summary. Rice Genotype Search and Summary. Molecular Breeding Knowledge Database. Created with the Personal Edition of HelpNDoc: News and information about help authoring tools and software. For example: Locus (OsG00048223), RAP Locus (Os03g0407400), MSU Locus (LOC_Os02g44360),. For example(case sensitive): HD, TGW. MBK Nip Locus (OsNipG0313111200.01), MBK R498 Locus (OsR498G0203315700.01). For example(case sensitive): Drought Tolerance, Blast Resistance. Project: All Rice3k MBK Japan174 SubTree Sample >= 20 30 40. Molecular Breeding Knowledgebase (MBKbase) is an integrated database for population next-generation sequencing, germplasm resources, phenotypic and various othergenomics data.
feature list: operation_0484
feature list: operation 2421
feature list: operation 2429
feature list: operation 3196
feature list: operation 3227
software help: help

MCMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0128
application sub category: topic 2830
application sub category: topic 3315
citation: ACSOMEGA.8B00572
citation: pmcid:PMC6644659
citation: pubmed:31458826
description: Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions | MCMap is a tool particularly well-suited for analyzing energy landscapes of transient macromolecular complexes. The program applies a Monte Carlo strategy, where the ligand moves randomly in the electrostatic field of the receptor. By applying importance sampling, the major interaction sites are mapped, resulting in a global distribution of ligand-receptor complexes. This approach displays the dynamic character of transiently interacting protein complexes where not a single complex but an ensemble of complexes better describes the protein interactions. The software provides a broad range of analysis options which allow for relating the simulations to experimental data and for interpreting them on a structural level
feature list: operation_0478
feature list: operation 2492

MCOT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0749
application sub category: topic 3169
citation: GKZ800
citation: pmcid:PMC6868382
citation: pubmed:31750523
description: A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. added a link to the publication · 92cb2e86. 3rd_party/jemalloc_win_x64_5.1.0
feature list: operation_0238
feature list: operation_0239
feature list: operation 2492

MCS2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0821
application sub category: topic 3407
citation: BTZ393
citation: pmcid:PMC6612898
citation: pubmed:31510702
description: Minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks | Codes and data of competitive methods for finding minimal cut sets of a metabolic network | Files for the work on metabolic networks with Leonid, Tamon, Cedric, Reza, Hooman, and Nafiseh | You need to have licensed MATLAB before running the scripts | There are implemenations of four approaches for enumerating MCSs here. You can run either of them by running its script followed by model name followed by target reaction followed by 1 or 0 which indicates prior network reduction. -1 stands for all reactions
feature list: operation 3660
license: GPL-3.0

MCScan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: This software provides a clustering module for viewing the relationship of colinear segments in multiple genomes (or heavily redundant genomes). It takes the predicted pairwise segments from dynamic programming (DAGchainer in particular) and then try to build consensus segments from a set of related, overlapping segments.

MCSeEd
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0654
application sub category: topic 3168
application sub category: topic 3173
application sub category: topic 3674
citation: S41598-019-51423-2
citation: pmcid:PMC6795852
citation: pubmed:31619715
description: A reference-free, whole genome profiling system to address cytosine/adenine methylation changes. Methods for investigating DNA methylation nowadays either require a reference genome and high coverage, or investigate only CG methylation. Moreover, no large-scale analysis can be performed for N6-methyladenosine (6 mA) at an affordable price. Here we describe the methylation content sensitive enzyme double-digest restriction-site-associated DNA (ddRAD) technique (MCSeEd), a reduced-representation, reference-free, cost-effective approach for characterizing whole genome methylation patterns across different methylation contexts (e.g., CG, CHG, CHH, 6 mA). MCSeEd can also detect genetic variations among hundreds of samples. MCSeEd is based on parallel restrictions carried out by combinations of methylation insensitive and sensitive endonucleases, followed by next-generation sequencing.
feature list: operation_0308
feature list: operation 3196
feature list: operation 3204

MCT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic 2640
application sub category: topic 3315
citation: BTZ312
citation: pmcid:PMC6612807
citation: pubmed:31510657
description: Summarizing the solution space in tumor phylogeny inference by multiple consensus trees | Algorithms for summarizing cancer phylogenies using multiple consensus trees | MCT-Solver - Multiple Consensus Tree Solver | Multiple Consensus Tree (MCT) is a problem that takes a set of input trees on the same set of vertices and an integer k as input, find k consensus trees and a k-clustering of the input trees such that the sum of the distance of each input tree to its corresponding consensus tree is minimized. MCT-Solver contains 3 approaches to this problem, Brute Force, MILP, and Coordinate Ascent
feature list: operation_0555
feature list: operation_0557
feature list: operation 3478

MD-LOVIs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 3068
application sub category: topic 3372
citation: S11030-019-10002-3
citation: pubmed:31659696
description: When global and local molecular descriptors are more than the sum of its parts. MD-LOVIs (acronym for Molecular Descriptors from LOcal Vertex Invariants and Related Maps) is a multi-platform software developed in the Java programming. …methods and tools for Chem-Bio-Med-Informatic Studies. MD-LOVIs (acronym for Molecular Descriptors from LOcal Vertex Invariants and Related Maps) is a multi-platform software developed in the Java programming language
feature list: operation_0394
feature list: operation 3436
feature list: operation 3659
feature list: operation 3891

MDCAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 3047
application sub category: topic 3335
application sub category: topic 3512
citation: FGENE.2019.00935
citation: pmcid:PMC6786093
citation: pubmed:31632446
description: A Computational Model to Predict the Causal miRNAs for Diseases. miRNA-disease causal association predictor. /main.py used for calculate causal miRNA-disease association potential score. /crossvalidation.py used for 10-fold cross validation.
feature list: operation_0463
feature list: operation 2428
feature list: operation 3792

MDDGlutar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0154
application sub category: topic_0601
application sub category: topic_0749
citation: s12859-018-2394-9
citation: pmcid:PMC7394328
citation: pubmed:30717647
description: Web server for identifying glutarylation sites.
feature list: operation_0417
feature list: operation 3755
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: introduction.php

MDFPtools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0176
application sub category: topic 2258
application sub category: topic 3047
application sub category: topic 3336
application sub category: topic 3474
citation: S10822-019-00252-6
citation: pubmed:31745704
description: Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge. This is a Python implementation of the molecular dynamics fingerprints (MDFP) methodology for building predictive models for phys-chem properties as delineated in our publication. This toolkit is described and applied to the SAMPL6 logP prediction challenge, with the results published here. Visit our documentation to learn details about installation, example workflow and API references.
feature list: operation_0337
feature list: operation 2476
feature list: operation 3893
license: MIT

MDMS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0078
application sub category: topic_0176
application sub category: topic 3068
application sub category: topic 3332
citation: JCC.26090
citation: pubmed:31660624
description: Software Facilitating Performing Molecular Dynamics Simulations. MDMS: Molecular Dynamics Made Simple; Python program facilitating performing Molecular Dynamics simulations of proteins. MDMS: Molecular Dynamics Made Simple. The idea behind MDMS design is that the beginnings should be easy - not exhausting. That is why this program accommodates everything that is required for getting realistic insights about protein/protein-ligand complexes through MD simulations
feature list: operation_0477
feature list: operation 2476
feature list: operation 3893
license: MIT

MDPBiome
type: SoftwareApplication
input: Count matrix
  type: FormalParameter
  additional type: data 3917
  encoding format: format 3746
output: Mathematical model
  type: FormalParameter
  additional type: data_0950
  encoding format: format 3033
output: Histogram
  type: FormalParameter
  additional type: data 3905
  encoding format: format 3508
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0091
application sub category: topic_0092
application sub category: topic 2269
application sub category: topic 3301
application sub category: topic 3474
author: https://orcid.org/0000-0002-1977-9777
citation: bty562
contributor: 0000-0001-6960-357X
description: MDPbiome is a software developed in R that uses Markov Decision Processes to create "policy prescriptions" for microbiome engineering. MDPbiome performs a variety of analysis describing the robustness of the prescription, as well as a variety of visualizations to assist in manual interpretation of the state transitions and biological understanding of a microbiome's dynamics.
feature list: operation_0004
feature list: operation_0335
feature list: operation_0337
feature list: operation 3432
feature list: operation 3480
feature list: operation 3695
feature list: operation 3731
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0002-8129-6506

MDiNE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2269
application sub category: topic 3170
application sub category: topic 3174
application sub category: topic 3697
citation: btz824
citation: pmcid:PMC7075537
citation: pubmed:31697315
description: A model to estimate differential co-occurrence networks in microbiome studies. (Note: This package is currently in development) Microbiome Differential Network Estimation (mdine) allows the estimation of OTU co-occurrence networks within two separate groups, where the networks are defined through precision matrices. The difference between the two precision matrices is also estimated, along with corresponding interval estimates. This work was developed in the Greenwood Lab at McGill University.
feature list: operation 3562
feature list: operation 3659

MEPSAnd
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0166
application sub category: topic_0602
citation: BTZ649
citation: pubmed:31418769
description: Minimum Energy Path Surface Analysis over n-dimensional surfaces | Molecular Modelling Group. Grupo de Modelado Molecular. Centro de Biologia Molecular 'Severo Ochoa' CBMSO, CSIC-UAM | bioweb: molecular modelling group / grupo de modelado molecular | [ http://www.cbm.csic.es/bioweb ] [ http://bioweb.cbm.uam.es ] | n-dimensional energy surfaces are becoming computationally accessible, yet interpreting their information is not straightforward. We present MEPSAnd, an open source GUI-based program that natively calculates minimum energy paths across energy surfaces of any number of dimensions. Among other features, MEPSAnd can compute the path through lowest barriers and automatically provide a set of alternative paths. MEPSAnd offers distinct plotting solutions as well as direct python scripting
feature list: operation 1816
license: GPL-3.0

MERCAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3305
citation: J.MEEGID.2019.104043
citation: pubmed:31683007
description: Visualising molecular epidemiology data combining genetic markers and drug resistance profiles. Molecular epidemiology uses genetic information from bacterial isolates to shed light on the population structure and dynamics of pathogens. Bacterial pathogens can now be studied by whole genome sequencing, but for some well-studied pathogens such as Mycobacterium tuberculosis a wealth of information is also available from other sources such as spoligotyping and multi-locus variable-number-tandem-repeats (VNTR). Isolates are also frequently tested for susceptibility to antibiotics. Methods of analysis are available for each type of data but it would be informative to combine multiple sources of information into a single analysis or visualisation. Here, we propose and implement a simple way to visualise genotypes along with drug resistance profiles for multiple drugs.
feature list: operation_0337
feature list: operation 3196
feature list: operation 3482

MERLoT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
citation: GKZ706
citation: pmcid:PMC6755101
citation: pubmed:31428793
description: Reconstructing complex lineage trees from scRNA-seq data using MERLoT | Reconstruct the lineage topology of a scRNA-seq differentiation dataset | MERLot: A MEthod for Reconstructing Lineage tree Topologies using scRNA-seq data | Benchmark and plotting scripts for the MERLoT paper | MERLot is a tool that can reconstruct the lineage tree topology that explains the emergence of different cell types from a progenitor population. MERLot is an R package than can reconstruct complex lineage tree topologies using coordinates for cells in a given manifold(like diffusion maps) as input | A collection of scripts that was used to generate and benchmark the simulations provided with the tool MERLoT. Download the expression matrices and parameter files via the GWDG FTP server. These will be used as examples for the various scripts | merlot_prosstt_deep_20190424.tar.gz
feature list: operation 3478
feature list: operation 3557
feature list: operation 3891
license: GPL-3.0

MERMAID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0176
application sub category: topic_0736
application sub category: topic_0820
citation: GKZ416
citation: pmcid:PMC6602572
citation: pubmed:31106328
description: Web server to prepare and run coarse-grained membrane protein dynamics.
feature list: operation_0244
feature list: operation 2476
feature list: operation 3431
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial.php
primary contact: Alejandro Giorgetti

MESSA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0623
application sub category: topic_0821
citation: CPBI.84
citation: pmcid:PMC6750024
citation: pubmed:31524991
description: Predicting Sequence Features, Function, and Structure of Proteins Using MESSA | MEta-Server for protein Sequence Analysis (MESSA) is a tool that facilitates widespread protein sequence analysis by gathering structural (local sequence properties and three-dimensional structure) and functional (annotations from SWISS-PROT, Gene Ontology terms, and enzyme classification) predictions for a query protein of interest. MESSA uses multiple well-established tools to offer consensus-based predictions on important aspects of protein sequence analysis. Being freely available for noncommercial users and with a user-friendly interface, MESSA serves as an umbrella platform that overcomes the absence of a comprehensive tool for predictive protein analysis. This article reveals how to access MESSA via the Web and shows how to input a protein sequence to analyze using the MESSA web server
feature list: operation 3092

MESSAR (MEtabolite SubStructure Auto-Recommender)
type: SoftwareApplication
input: Mass spectrum
  type: FormalParameter
  additional type: data_0943
input: Spectrum
  type: FormalParameter
  additional type: data 3483
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3172
description: Despite the increasing importance of non-targeted metabolomics to answer various life science questions, extracting biochemically relevant information from metabolomics spectral data is still an incompletely solved problem. Our framework captures potential relationships between spectral features and substructures learned from public spectral libraries. These associations are used to recommend substructures for any unknown mass spectrum. Our method does not require any predefined metabolite candidates, and therefore it can be used for the partial identification of unknown unknowns.
feature list: operation 3801
feature list: operation 3803

METACLUSTER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3407
citation: btz021
citation: pmcid:PMC6735823
citation: pubmed:30657869
description: R package for context-specific expression analysis of metabolic gene clusters.
feature list: operation_0313
feature list: operation 3223
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: EducatedGuess.ai

MEXCOwalk
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0199
application sub category: topic 2640
citation: BTZ655
citation: pubmed:31432076
description: Mutual Exclusion and Coverage Based Random Walk to Identify Cancer Modules | This is the original repository for the MEXCOwalk paper | The evaluation file can also be run with multiple models and compared to MEXCOwalk. Simply store the models in 'out/connected_components_isolarge/model_x' and add the model name to the evaluations section in the evaluation file as follows:
feature list: operation 1812
feature list: operation 3501

MG-RAST API explorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0637
application sub category: topic_0769
application sub category: topic 3168
application sub category: topic 3174
application sub category: topic 3308
citation: S12859-019-2993-0
citation: pmcid:PMC6842160
citation: pubmed:31703549
description: An on-ramp for RESTful query composition. an on-ramp for learning to use the MG-RAST API. MG-RAST (the Metagenomics RAST) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server provides upload, quality control, automated annotation and comparative analysis for shotgun and amplicon metagenomic samples as well as metatranscriptomes. MG-RAST API Explorer -- an on-ramp for learning to use the MG-RAST API. An object store for scientific data. MG-RAST provides a RESTful API at https: api.mg-rast.org. workflow and resource management system for bioinformatics data analysis.
feature list: operation_0224
feature list: operation_0337
feature list: operation_0362
feature list: operation 3192

MGERT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0769
application sub category: topic_0798
citation: S13100-019-0163-6
citation: pmcid:PMC6515669
citation: pubmed:31114637
description: Mobile Genetic Elements Retrieving Tool Pipeline (MGERT) for retrieving coding sequences of mobile genetic elements from genome assemblies.
feature list: operation_0427
feature list: operation_0525
feature list: operation 2422
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0002-6329-2421

MGLEX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
application sub category: topic 3297
application sub category: topic 3303
application sub category: topic 3697
application sub category: topic 3837
citation: PEERJ.PREPRINTS.2626V2
citation: PEERJ.PREPRINTS.2626V3
description: A probabilistic model to recover individual genomes from metagenomes. MGLEX - MetaGenome Likelihood EXtractor. This Python Package provides a probabilistic model to classify nucleotide sequences in metagenome samples. It was developed as a framework to help researchers to reconstruct individual genomes from such datasets using custom workflows and to give developers the possibility to integrate the model into their programs. MGLEX – A Python Package for Probabilistic Modeling and Binning of Metagenomes. We recommend to create a Python virtual installation enviroment for MGLEX. In order to do so, install the venv package for your Python version (e.g. the Debian package python3.4-venv), if not included (or use virtualenv). The following command will make use of the installed system packages
feature list: operation_0310
feature list: operation 3431
feature list: operation 3472
feature list: operation 3731
license: GPL-3.0

MGMM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2269
application sub category: topic 2885
citation: s12859-022-04740-9
citation: pmcid:PMC9158227
citation: pubmed:35650523
description: Parameter estimation and classification for Gaussian Mixture Models (GMMs) in the presence of missing data.
feature list: operation 3432
feature list: operation 3435
feature list: operation 3557
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: MGMM.pdf

MGOB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0091
application sub category: topic_0102
application sub category: topic 3293
citation: foz058
citation: pmcid:PMC6904324
citation: pubmed:31397853
description: The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae | The Methylotroph Gene Order Browser (MGOB) is an online tool for visualising the syntenic context of any gene from several yeast genomes - Copyright Kevin Byrne - ygob@ucd.ie - Wolfe Laboratory, Conway Institute, University College Dublin, Dublin 4, Ireland
feature list: operation 3208
feature list: operation 3216
feature list: operation 3501

MGnify
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic_0769
application sub category: topic 2229
application sub category: topic 3174
application sub category: topic 3697
citation: gkz1035
citation: pmcid:PMC7145632
citation: pubmed:31696235
description: The microbiome analysis resource in 2020. MGnify (http: www.ebi.ac.uk metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility.
feature list: operation_0310
feature list: operation 3184
feature list: operation 3731

MHCII
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0749
application sub category: topic_0781
application sub category: topic_0804
application sub category: topic 3292
citation: https://doi.org/10.1101/795427
description: Multi Epitope Vaccine Prediction Against Aichi Virus using Immunoinformatic Approach. IEDB recommended 2.22 IEDB recommended 2.18 Consensus 2.22 Consensus 2.18 NetMHCIIpan 3.2 NetMHCIIpan 3.1 NN-align 2.3 (NetMHCII 2.3) NN-align 2.2 (NetMHCII 2.2) SMM-align (NetMHCII 1.1) Combinatorial library Sturniolo Help on prediction method selections. Enter protein sequence(s) in FASTA format. Or select file containing sequence(s). or as whitespace-separated sequences.
feature list: operation_0252
feature list: operation_0416
feature list: operation_0482

MHCSeqNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 2830
citation: s12859-019-2892-4
citation: pmcid:PMC6540523
citation: pubmed:31138107
description: Deep neural network model for universal Major Histocompatibility Complex (MHC) binding prediction.
feature list: operation_0252
feature list: operation 3227
feature list: operation 3631
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Computational Molecular Biology Group, Chulalongkorn University

MHCquant
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0769
application sub category: topic 2830
application sub category: topic 3520
citation: ACS.JPROTEOME.9B00313
citation: pubmed:31589052
description: Automated and Reproducible Data Analysis for Immunopeptidomics. MHCquant: Identify and quantify peptides from mass spectrometry raw data.
feature list: operation 3634
feature list: operation 3643
feature list: operation 3649

MIAmS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 2885
application sub category: topic 3168
citation: BTZ797
citation: pubmed:31647522
description: Microsatellite instability detection on NGS amplicons data. Workflow for detecting microsatellite instability by next-generation sequencing on amplicons. MIAmS: Microsatellites Instability by AMplicon Sequencing.
feature list: operation 3435

MIAmaxent
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0605
application sub category: topic_0610
application sub category: topic 2269
citation: ECE3.5654
citation: pmcid:PMC6854112
citation: pubmed:31832144
description: Variable transformation and model selection for species distribution models. A reproducible paper describing the MIAmaxent R package. Read our open-access paper in Ecology and Evolution introducing MIAmaxent: https://doi.org/10.1002/ece3.5654. Maxent software for modeling species niches and distributions. The file 'miamaxent-ms. MIAmaxent is intended primarily for maximum entropy distribution modeling (Phillips et al., 2006; Phillips et al., 2017), and provides an alternative to the standard methodology for training, selecting, and using models. Use this site to download Maxent software for modeling species niches and distributions by applying a machine-learning technique called maximum entropy modeling.
feature list: operation 3435
feature list: operation 3659
feature list: operation 3664

MIC_Locator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0140
application sub category: topic_0605
application sub category: topic 2229
application sub category: topic 3382
citation: S12859-019-3136-3
citation: pmcid:PMC6815465
citation: pubmed:31655541
description: A novel image-based protein subcellular location multi-label prediction model based on multi-scale monogenic signal representation and intensity encoding strategy. The dataset for MIC_Locator can be downloaded from the website (https://pan.baidu.com/s/1dvvyT9OuJUcQYkCxidABDw)
feature list: operation_0321
feature list: operation 2489
feature list: operation 3092

MIENTURNET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0605
application sub category: topic_0659
application sub category: topic 3512
citation: S12859-019-3105-X
citation: pmcid:PMC6829817
citation: pubmed:31684860
description: An interactive web tool for microRNA-target enrichment and network-based analysis. BACKGROUND:miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than one miRNA. Therefore, it has become indispensable to shorten the long list of miRNA-target interactions to put in the spotlight in order to gain insight into understanding the regulatory mechanism orchestrated by miRNAs in various cellular processes. A reasonable solution is certainly to prioritize miRNA-target interactions to maximize the effectiveness of the downstream analysis. RESULTS:We propose a new and easy-to-use web tool MIENTURNET (MicroRNA ENrichment TURned NETwork) that receives in input a list of miRNAs or mRNAs and tackles the problem of prioritizing miRNA-target interactions by performing a statistical analysis followed by a fully featured network-based visualization and analysis
feature list: operation_0463
feature list: operation 2436
feature list: operation 3792

MIGRATE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0097
application sub category: topic 3056
application sub category: topic 3500
citation: pnas.1810239116
citation: genetics.109.112532
citation: pmcid:PMC2870966
citation: pmcid:PMC6442577
citation: pubmed:20176979
citation: pubmed:30867282
description: Estimates effective population sizes,past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes, and population divergences or admixture.
feature list: operation_0487
feature list: operation_0547
feature list: operation 3446
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: about.html
software help: tutorials.html

MILAMP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic 3382
application sub category: topic 3474
citation: TCBB.2019.2936846
citation: pubmed:31443048
description: Multiple Instance Prediction of Amyloid Proteins | Software and Data Downloads — Personal Webpage documentation | Note: This page will be discontinued. Please visit my new webpage HERE and update your bookmarks | Link to my GitHub profile: HERE Here is a list of the software developed in my lab | AMAP: Antimicrobial activity prediction | MILAMP: Multiple Instance Learning of Amyloid Proteins. Webserver available HERE. Code available HERE
feature list: operation_0267
feature list: operation_0303
feature list: operation 2492

MIMIC-CXR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3384
application sub category: topic 3452
application sub category: topic 3489
citation: S41597-019-0322-0
citation: pmcid:PMC6908718
citation: pubmed:31831740
description: De-identified publicly available database of chest radiographs with free-text reports. If you use the MIMIC-CXR Database in your work, please cite the following publication:. MIMIC-CXR: A large publicly available database of labeled chest radiographs. Johnson AEW, Pollard TJ, Berkowitz S, Greenbaum NR, Lungren MP, Deng C-Y, Mark RG, Horng S. arXiv.. Available from: https://arxiv.org
feature list: operation 3443
feature list: operation 3553

MIND
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3518
citation: btz619
citation: pmcid:PMC7523682
citation: pubmed:31400192
description: Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression | Using Multiple Measurements of Tissue to Estimate Subject- And Cell-Type-Specific Gene Expression via Deconvolution | MIND (Multi-measure INdividual Deconvolution) | MIND is a method to glean insights from bulk gene expression. It borrows information across multiple measurements of the same tissue per subject, such as multiple regions of the brain, using an empirical Bayes approach to estimate subject- and cell-type-specific gene expression via deconvolution
feature list: operation 3232
feature list: operation 3629
feature list: operation 3658

The MINERVA Platform
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 2259
application sub category: topic 3342
application sub category: topic 3391
citation: j.envpol.2019.04.005
citation: npjsba.2016.20
citation: big.2015.0057
citation: bbz067
citation: btz286
citation: pmcid:PMC4932659
citation: pmcid:PMC5516855
citation: pmcid:PMC6821317
citation: pmcid:PMC7373180
citation: pubmed:27441714
citation: pubmed:28725475
citation: pubmed:30991279
citation: pubmed:31074494
citation: pubmed:31273380
description: The MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format, including files produced using CellDesigner or SBGN editors. Visualization of uploaded networks generated by the platform is accessible via a web browser to all viewers with the weblink to the resource. The MINERVA Platform is a webservice using the Java Server Faces 2 technology. The server side, including data parsing, integration, annotation and verification, is implemented in Java. The platform uses the Postgres SQL database for data storage and the Hibernate framework as a middle layer between web server and database. The user web-interface is generated using React.js. The displayed content is visualized by OpenLayers API, dedicated JavaScript and CSS.
feature list: operation_0571
feature list: operation 2426
feature list: operation 3434
feature list: operation 3926
is accessible for free: true
license: AGPL-3.0
software help: minerva.uni.lu
software version: 13.1.3
software version: 13.2.0
software version: 14.0.13
software version: 15.0.3
software version: 16.4.0
software version: 17.1.3
software version: 18.1.1
software version: 19.1.0

MINES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0160
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3512
citation: RNA.072785.119
citation: pmcid:PMC6913132
citation: pubmed:31624092
description: Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base-specific resolution. (m)6A (I)dentification Using (N)anopor(E) (S)equencing. Tombo(v1.4) Commands Prior to MINES:. python cDNA_MINES.py --fraction_modified output_filename.fraction_modified_reads.plus.wig.bed --coverage output_filename.coverage.plus.bedgraph --output m6A_output_filename.bed --ref REF.fa.
feature list: operation_0239
feature list: operation_0417
feature list: operation 3644

MIRIA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0621
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: S12859-019-3242-2
citation: pmcid:PMC6923819
citation: pubmed:31861975
description: A webserver for statistical, visual and meta-analysis of RNA editing data in mammals. BACKGROUND:Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have developed several new pipelines and software packages to identify RNA editing sites with a focus on downstream statistical analysis and functional interpretation. RESULTS:Here, we developed a user-friendly public webserver named MIRIA that integrates statistics and visualization techniques to facilitate the comprehensive analysis of RNA editing sites data identified by the pipelines and software packages.
feature list: operation_0337
feature list: operation 2495
feature list: operation 3096

MIRKB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3300
application sub category: topic 3305
application sub category: topic 3335
application sub category: topic 3382
citation: BAZ125
citation: pmcid:PMC6830040
citation: pubmed:31688939
description: A myocardial infarction risk knowledge base. Myocardial Infarction Risk Knowledge Base. MIRKB (the Myocardial Infarction Risk Knowledge Base) is a database that collected single factors, combined factors, and risk models which are article-supported to be associated with the risk assessment, diagnosis, prognosis, and treatment of MI in human. The goal of MIKB was to improve the efficiency of MI research. MI is a common cardiovascular disease and a leading cause of death worldwide. It can be classified into many types according to the disease phase, lesion range, ECG expression, infarction location, and clinical type
feature list: operation 2421
feature list: operation 2422
feature list: operation 3454

MIRUReader
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0625
application sub category: topic_0632
application sub category: topic 2885
application sub category: topic 3305
citation: BTZ771
citation: pubmed:31603462
description: Fast in-silico MIRU-VNTR typing directly from long sequencing reads. In-silico MIRU-VNTR typing using long reads. Identify 24-locus MIRU-VNTR for Mycobacterium tuberculosis complex (MTBC) directly from long reads generated by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). Also work on assembled genome.
feature list: operation_0310
feature list: operation 3196
feature list: operation 3227
license: MIT

MITK-ModelFit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3375
application sub category: topic 3384
application sub category: topic 3444
citation: s12859-018-2588-1
citation: pmcid:PMC6335810
citation: pubmed:30651067
description: Generic open-source framework for model fits and their exploration in medical imaging - design, implementation and application on the example of DCE-MRI.
feature list: operation 3629
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows

MITRE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic 3474
application sub category: topic 3697
citation: S13059-019-1788-Y
citation: pmcid:PMC6721208
citation: pubmed:31477162
description: Inferring features from microbiota time-series data linked to host status | The Microbiome Interpretable Temporal Rule Engine | Input code and results from simulations supporting the MITRE paper | Supporting files for the Microbiome Interpretable Temporal Rule Engine manuscript | MITRE learns predictive models of patient outcomes from microbiome time-series data in the form of short lists of interpretable rules | This repository includes the configuration files used to set up simulations for the MITRE manuscript, and results from those simulations, with a few useful auxiliary files | MITRE will load data from Bokulich, N. A., et al., "Antibiotics, birth mode, and diet shape microbiome maturation during early life." Science Translational Medicine 8(343): 343ra82, which is packaged with MITRE
feature list: operation_0337
feature list: operation 1812
feature list: operation 3436
license: GPL-3.0

MIXR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3293
application sub category: topic 3308
application sub category: topic 3512
citation: PNAS.1814995116
citation: pmcid:PMC6561249
citation: pubmed:31113885
description: Mismatching Isoform eXon Remover.
feature list: operation_0499
feature list: operation_0544
feature list: operation 3258
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Sara L. Sawyer
primary contact: William H. Press

MKpLMM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3384
application sub category: topic 3577
citation: btz822
citation: pmcid:PMC7523642
citation: pubmed:31693075
description: Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data. MOTIVATION:The use of human genome discoveries and other established factors to build an accurate risk prediction model is an essential step towards precision medicine. While multi-layer high-dimensional omics data provide unprecedented data resources for prediction studies, their corresponding analytical methods are much less developed. RESULTS:We present a multi-kernel linear mixed model with adaptive lasso (MKpLMM), a predictive modeling framework that extends the standard linear mixed models widely used in genomic risk prediction, for multi-omics data analysis. MKpLMM can capture not only the predictive effects from each layer of omics data but also their interactions via using multiple kernel functions.

ML-Force
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0153
application sub category: topic_0176
application sub category: topic_0621
citation: S12859-019-3092-Y
citation: pmcid:PMC6880518
citation: pubmed:31775608
description: Potential based, spatial simulation of dynamically nested particles. Source repository for the publication "Potential based, spatial simulation of dynamically nested particles" in BMV Bioinformatics. ML-Force source code added · 1e971b94.
feature list: operation 2476

ML-morph
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic 3298
application sub category: topic 3382
citation: https://doi.org/10.1101/769075
description: A Fast, Accurate and General Approach for Automated Detection and Landmarking of Biological Structures in Images | Machine-learning-based morphometrics | Machine-learning tools for landmark-based morphometrics | Porto & Voje (2019) A fast, accurate and general model for automated landmarking of biological images. Submitted | Also note that while ml-morph can handle multiple image file formats, some care is needed with regards to the presence of special characters in image filenames. So far, we have only had problems with &, but it is possible that other special characters might lead the software to throw out an error

MLC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3518
citation: https://doi.org/10.1101/651042
description: Metric Learning on Expression Data for Gene Function Prediction.
feature list: operation 3463
feature list: operation 3501
feature list: operation 3766
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Stavros Makrodimitris

MLCS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0081
application sub category: topic_0157
application sub category: topic_0654
citation: BTZ725
citation: pubmed:31584616
description: A Fast and Memory Efficient MLCS Algorithm by Character Merging for DNA Sequences Alignment. This is a fast MLCS algorithm for DNA sequence
feature list: operation_0232
feature list: operation_0292
feature list: operation_0306

MLDSP-GUI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0637
application sub category: topic_0654
application sub category: topic 3474
citation: https://doi.org/10.1101/745406
description: An alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis | An alignment-free standalone tool with interactive graphical user interface for DNA sequence comparison and analysis
feature list: operation_0337
feature list: operation 3460

MLM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0593
application sub category: topic_0749
citation: btz421
citation: pmcid:PMC6954661
citation: pubmed:31116391
description: Morais-Lima-Martin (MLM) algorithm for data splitting for classification applications in spectrochemical analyses employing a random-mutation Kennard-Stone algorithm approach.
feature list: operation 3359
feature list: operation 3891
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

MLML2R
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3295
application sub category: topic 3518
application sub category: topic 3674
citation: sagmb-2018-0031
citation: pubmed:30653470
description: R package for maximum likelihood estimation of DNA methylation and hydroxymethylation proportions.
feature list: operation 1812
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: MLML2R
software version: 0.3.2
primary contact: Samara Kiihl

MLSTar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic 3305
application sub category: topic 3673
application sub category: topic 3796
citation: PEERJ.PREPRINTS.26630V2
description: Automatic multilocus and core genome sequence typing in R. An easy way of MLSTyping your genomes in R. This R package allows you to easily determine the Multi Locus Sequence Type (MLST) of your genomes. It also works as an interface between PubMLST through their RESTful API, so you don't have to bother downloading and collecting files: the application does it automatically. Today the package works in Unix-based systems. If you use MLSTar in your publications, please cite:. Note: cgMLST and wgMLST are not yet fully supported since the RESTful API interphase for theses cases is a little different than the one for the standard 7 loci schemes. See issues#11 for more details
feature list: operation 3227
feature list: operation 3431
feature list: operation 3840
license: MIT

MLVAType
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0632
application sub category: topic 2885
application sub category: topic 3519
application sub category: topic 3673
citation: JOURNAL.PONE.0225848
citation: pmcid:PMC6905556
citation: pubmed:31825986
description: Backward compatibility of whole genome sequencing data with MLVA typing using a new MLVAtype shiny application for Vibrio cholerae. python-dev (sudo apt-get install python-dev),. regex (https://launchpad.net/ubuntu/+archive/primary/+files/python-regex_0.1.20170117.orig.tar.gz).
feature list: operation_0308
feature list: operation_0310
feature list: operation 2404

ML Repo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3174
application sub category: topic 3474
application sub category: topic 3697
citation: GIZ042
citation: pmcid:PMC6493971
citation: pubmed:31042284
description: Microbiome Learning Repo (ML Repo) - public repository of microbiome regression and classification tasks
feature list: operation 3192
feature list: operation 3431
feature list: operation 3659
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-8205-2511

MLatom
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3314
application sub category: topic 3474
application sub category: topic 3570
citation: jcc.26004
citation: pubmed:31219626
description: Program package for quantum chemical research assisted by machine learning.
feature list: operation 3659
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: manual
primary contact: Dr. Pavlo O. Dral

MLME: Machine Learning Made Easy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Machine Learning Made Easy (MLme) is a novel tool that simplifies machine learning (ML) for researchers. By integrating four essential functionalities, namely data exploration, AutoML, CustomML, and visualization, MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. MLme serves as a valuable resource that empowers researchers of all technical levels to leverage ML for insightful data analysis and enhance research outcomes. By simplifying and automating various stages of the ML workflow, it enables researchers to allocate more time to their core research tasks, thereby enhancing efficiency and productivity.

MM-WHS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3335
application sub category: topic 3384
application sub category: topic 3444
citation: j.media.2019.101537
citation: pmcid:PMC6839613
citation: pubmed:31446280
description: Evaluation of algorithms for Multi-Modality Whole Heart Segmentation | Multi-Modality Whole Heart Segmentation Challenge | MM-WHS: Multi-Modality Whole Heart Segmentation | Accurate computing, modeling and analysis of the whole heart substructures is important in the development of clinical applications. Segmentation and registration of whole heart images is however challenging and still relies heavily on manual work, which is time-consuming and prone to errors | For evaluation of the test data, the participants should prepare a brief description of their algorithm and email with the segmentation results of the test datasets to the organizers
feature list: operation_0337
feature list: operation 3435
feature list: operation 3891

MM3
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0769
application sub category: topic 3382
application sub category: topic 3474
citation: https://doi.org/10.1101/810036
description: Mother machine image analysis with MM3. Version 3 of Python mother machine analysis code. MM3 at University of California, San Diego. MM3 at University of California, San Diego for Fall 2019 on Piazza, a free Q&A platform for students and instructors. mm3 is a image analysis pipeline for mother machine experiments. It takes as input raw timelapse images and produces as output cell objects containing information such as elongation rate, birth size, etc. There is support for fluorescent planes. Segmentation and tracking software for mother machine experiments. The name Piazza comes from the Italian word for plaza--a common city square where people can come together to share knowledge and ideas. We strive to recreate that communal atmosphere among students and instructors
feature list: operation 3443
feature list: operation 3454

MMCL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0593
application sub category: topic 3315
application sub category: topic 3384
application sub category: topic 3398
application sub category: topic 3452
citation: https://doi.org/10.1101/815977
description: GPU-accelerated mesh-based Monte Carlo photon transport simulations. ===============================================================================. = Mesh-based Monte Carlo (MMC) =. = Supporting both OpenCL and Multi-threading with SSE4 =. A GPU-accelerated photon transport simulator. Download v2019.4 or Nightly-build. "mmc -L" or "mmclab('gpuinfo')" to list). Designing MATLAB-streamlined MC-based analysis using MCXLAB and MMCLAB.
feature list: operation_0337
feature list: operation 3431
feature list: operation 3435

MMseqs2
type: SoftwareApplication
input: Sequence set
  type: FormalParameter
  additional type: data_0850
  encoding format: format 2182
  encoding format: format 2200
input: Sequence set
  type: FormalParameter
  additional type: data_0850
  encoding format: format 2182
  encoding format: format 2200
input: Sequence set
  type: FormalParameter
  additional type: data_0850
  encoding format: format 2182
  encoding format: format 2200
output: Taxonomy
  type: FormalParameter
  additional type: data 3028
output: Sequence cluster
  type: FormalParameter
  additional type: data 1235
output: Sequence search results
  type: FormalParameter
  additional type: data_0857
  encoding format: format 1333
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0077
application sub category: topic_0078
application sub category: topic_0080
application sub category: topic_0623
application sub category: topic_0637
application sub category: topic 3174
citation: nbt.3988
citation: s41467-018-04964-5
citation: s41592-025-02819-8
citation: btab184
citation: bty1057
citation: https://doi.org/10.1101/079681
citation: https://doi.org/10.1101/2020.11.27.401018
citation: 2024.11.13.623350v1
citation: pmcid:PMC6026198
citation: pmcid:PMC6691333
citation: pmcid:PMC8479651
citation: pubmed:29035372
citation: pubmed:29959318
citation: pubmed:30615063
citation: pubmed:33734313
description: MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed. MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity.
feature list: operation_0291
feature list: operation_0292
feature list: operation_0346
feature list: operation 3460
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: Tutorials
software help: wiki

MNE-Python
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3384
application sub category: topic 3444
citation: PEERJ.PREPRINTS.27988V1
description: Software and resources for experiments and data analysis of MEG and EEG data | Installation — contents — MNE 0.19.1 documentation | The official home of the Python Programming Language | Notice: While Javascript is not essential for this website, your interaction with the content will be limited. Please turn Javascript on for the full experience | MNE-Python is an open-source Python module for processing, analysis, and visualization of functional neuroimaging data (EEG, MEG, sEEG, ECoG, and fNIRS) | Python is a programming language that lets you work quickly and integrate systems more effectively | Join the official 2019 Python Developers Survey Start the survey!
feature list: operation_0337
license: Proprietary
software help: install mne python.html

MOAD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3068
application sub category: topic 3336
citation: J.JMB.2019.05.024
citation: pmcid:PMC6589129
citation: pubmed:31125569
description: Mother of All Databases (MOAD) - Polypharmacology Tools and Their Utility in Drug Repurposing.
feature list: operation_0482
feature list: operation 2575
feature list: operation 2950
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: www.bindingmoad.org
software help: faq
primary contact: Heather A. Carlson

MOAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3673
citation: btx700
description: Efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool.
feature list: operation 1812
feature list: operation 3227
feature list: operation 3798
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: !page-usage
primary contact: Mark Gerstein

MOBFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: MOBFinder: a tool for MOB typing for plasmid metagenomic fragments based on language model

MOBscan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0160
application sub category: topic_0623
citation: 978-1-4939-9877-7 21
citation: pubmed:31584171
description: Automated Annotation of MOB Relaxases. Please, fill the submission form below and select the FASTA file containing the amino acid sequences. Your data is being processed. Please be patient as, depending on the number of sequences uploaded, it could take a few minutes
feature list: operation_0578
feature list: operation 2421
feature list: operation 3192

MOLGENIS Research
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3068
application sub category: topic 3303
application sub category: topic 3697
citation: bty742
citation: pmcid:PMC6419911
citation: pubmed:30165396
description: Web-application to collect, manage, analyze, visualize and share large and complex biomedical datasets, without the need for advanced bioinformatics skills.
feature list: operation 3501
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: molgenis.github.io
primary contact: Morris A. Swertz

MOLI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3474
citation: BTZ318
citation: pmcid:PMC6612815
citation: pubmed:31510700
description: Multi-omics late integration with deep neural networks for drug response prediction | MOTIVATION:Historically, gene expression has been shown to be the most informative data for drug response prediction. Recent evidence suggests that integrating additional omics can improve the prediction accuracy which raises the question of how to integrate the additional omics. Regardless of the integration strategy, clinical utility and translatability are crucial. Thus, we reasoned a multi-omics approach combined with clinical datasets would improve drug response prediction and clinical relevance. RESULTS:We propose MOLI, a multi-omics late integration method based on deep neural networks. MOLI takes somatic mutation, copy number aberration and gene expression data as input, and integrates them for drug response prediction
feature list: operation 3557

MONET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3360
citation: https://doi.org/10.1101/611418
description: Toolbox integrating top-performing methods for NEtwork MOdularisation.
feature list: operation 3216
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Mattia Tomasoni
primary contact: Sven Bergmann

MOODA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic 3895
citation: https://doi.org/10.1101/761320
description: Design and assembly of DNA molecules using multi-objective optimisation | A DNA design and assembly method based on multi-objective optimization | MOODA: Multi-Objective Optimization for DNA sequence Design and Assembly | A manufacturing-aware sequence optimizer | Write a MOODA configuration file. A .yaml file defining operators, objective functions, assemblies strategy and their parameters, this is how a MOODA configuration file looks like:
feature list: operation 2425
feature list: operation 3745
license: MIT

MOOMIN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3315
application sub category: topic 3407
citation: btz584
citation: pmcid:PMC9883724
citation: pubmed:31504164
description: Mathematical explOration of 'Omics data on a MetabolIc Network | MOOMIN is a tool for analysing differential expression data | MOOMIN (Mathematical explOration of Omics data on a MetabolIc Network) is a tool for analysing differential expression data. It takes as its input a metabolic network and the results of a DE analysis: a posterior probability of differential expression and a (logarithm of a) fold change for a list of genes. It then forms a hypothesis of a metabolic shift, determining for each reaction its status as "increased flux", "decreased flux", or "no change". These are expressed as colours: red for an increase, blue for a decrease, and grey for no change. See the paper for full details: https://doi.org/10.1093/bioinformatics/btz584
feature list: operation 3223
feature list: operation 3501
feature list: operation 3660
license: MIT

MOSClip
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3295
citation: gkz324
citation: pmcid:PMC6698707
citation: pubmed:31049575
description: Multi-Omic and Survival pathway analysis for the identification of survival associated gene and module.
feature list: operation_0417
feature list: operation_0533
feature list: operation 3207
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: MOSClip
primary contact: Paolo Martini

MOST-visualization
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3407
citation: btx240
citation: pubmed:28430868
description: Software for producing automated textbook-style maps of genome-scale metabolic networks.
feature list: operation_0533
feature list: operation 3660
feature list: operation 3803
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
software help: tutorials.html
primary contact: Desmond S. Lun

MOTS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0634
citation: MHEALTH.2019.09.03
citation: pmcid:PMC6789201
citation: pubmed:31620462
description: Mobile training and support (MOTS) service-using technology to increase Ebola preparedness of remotely-located community health workers (CHWs) in Sierra Leone. As in many African countries, the Community Health Worker (CHW) is the backbone of the healthcare system, and the focus and objective of the Mobile Training and Support (MOTS) project will be strengthening this network to ensure preparedness for Ebola vaccine campaigns and outbreak response. The project will set up a MOTS service that is the veh….
license: Apache-2.0

MPF-BML
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0078
application sub category: topic 2269
application sub category: topic 3474
citation: BTZ925
citation: pubmed:31851308
description: A standalone GUI-based package for maximum entropy model inference. Minimum Probability Flow-Boltzmann Machine Learning (MPF-BML) standalone GUI-based application for the inference of maximum entropy distribution parameters. MPF-BML: A standalone GUI-based cross-platform package for maximum entropy model inference. MPF-BML-GUI is a standalone cross-platform package which features an easy-to-use GUI. The package only requires the input data (protein sequence data or data of multiple configura-tions of a complex system with large number of variables) and returns the maximum entropy model parameters inferred using the MPF-BML method
license: MIT

MPIC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 2269
application sub category: topic 3068
application sub category: topic 3360
application sub category: topic 3379
citation: FGENE.2019.00830
citation: pmcid:PMC6759478
citation: pubmed:31620162
description: Molecular Prognostic Indicators in Cirrhosis Database for Clinical Context-Specific in Silico Prognostic Biomarker Validation. Molecular Prognostic Indicators in Cirrhosis. Database for clinical context-specific in silico prognostic biomarker validation. This is a system that enables quick and easy assessment of user’s prognostic gene signature in various liver disease patient cohorts for a specific clinical outcome
feature list: operation 2428
feature list: operation 2495

MPRAnalyze
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3170
citation: S13059-019-1787-Z
citation: pmcid:PMC6717970
citation: pubmed:31477158
description: Statistical framework for massively parallel reporter assays | Statistical Analysis of MPRA data | MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes
feature list: operation 3200
feature list: operation 3501
feature list: operation 3799
license: GPL-3.0

MPRAnator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0749
application sub category: topic 2885
application sub category: topic 3518
citation: btw584
citation: pmcid:PMC5198521
citation: pubmed:27605100
description: Web-based tool for the design of massively parallel reporter assay experiments.
feature list: operation_0438
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation
primary contact: Ilias Georgakopoulos-Soares
primary contact: Martin Hemberg

MPRAscore
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
citation: BTZ591
citation: pubmed:31359027
description: Robust and non-parametric analysis of massively parallel reporter assays | MPRAscore: Robust and non-parametric analysis of massively parallel reporter assays (MPRA) | MPRAscore infers allele-specific effects on transcription from MPRA data. MPRAscore uses a weighted, variance-regularized method to calculate variant effect sizes robustly, and a permutation approach to test for significance without assuming normality or independence

MPRDock
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic_0176
application sub category: topic 2275
citation: BTZ388
citation: pubmed:31086984
description: Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models.
feature list: operation_0477
feature list: operation_0482
feature list: operation 3899
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Lab of Bioinformatics and Molecular Modeling

MPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0769
application sub category: topic 2269
application sub category: topic 3360
citation: PEERJ.PREPRINTS.511V2
citation: pmcid:PMC4349052
citation: pubmed:25755929
description: Language workbench user interfaces for data analysis. The Domain-Specific Language Creator by JetBrains. Use MPS platform to create your own domain-specific language that speak to your business needs. Use non-textual notation with projectional editing. BDVal for MPS is an MPS plugin designed to help you configure BDVal projects. BDVal for MPS makes it easier to develop and validate predictive models in high-throughput datasets. When the product is highly complex and the developers aren’t experts in your business domain. MPS helps even unfamiliar developers understand the system immediately
feature list: operation 3096
feature list: operation 3359

MPS-Db
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3336
application sub category: topic 3375
application sub category: topic 3379
citation: https://doi.org/10.1101/776500
description: Applications of the Microphysiology Systems Database for Experimental ADME-Tox and Disease Models | The MPS-Db aggregates MPS data with linked preclinical and clinical databases for analysis in the context of human exposure. Built in tools enable the assessment of the reproducibility and transferability of MPS models, while computational models are being developed to enhance the value of MPS models for understanding disease mechanisms, compound toxicity, and prediction of drug pharmacokinetics (PK)
feature list: operation 3436

MR-Base
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0154
application sub category: topic_0625
application sub category: topic 3517
citation: WELLCOMEOPENRES.15334.1
citation: elife.34408
citation: pmcid:PMC5976434
citation: pmcid:PMC6694718
citation: pubmed:29846171
citation: pubmed:31448343
description: Using the MR-Base platform to investigate risk factors and drug targets for thousands of phenotypes | This repository contains the case studies associated with the manuscript "Using the MR-Base platform to investigate risk factors and drug targets for thousands of phenotypes" | 2-sample Mendelian Randomisation | MR-base is a database and analytical platform for Mendelian randomization being developed by the MRC Integrative Epidemiology Unit at the University of Bristol
feature list: operation_0488
feature list: operation 3659
license: MIT

MR-Clust
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 2885
application sub category: topic 3305
application sub category: topic 3517
citation: https://doi.org/10.1101/2019.12.18.881326
description: Clustering of genetic variants in Mendelian randomization with similar causal estimates. R package for investigating clustered heterogeneity in Mendelian randomization (MR) analyses. mr_clust_em - performs expectation-maximisation (EM) based model fitting of the MR-Clust mixture model. Genetic variants which recover similar estimates of the causal effect of the risk-factor on the outcome - i.e. their ratio-estimates are similar in direction, magnitude and precision - can form distinct clusters in MR analyses. We call this `clustered heterogeneity'. Each cluster might represent a distinct pathway with which the risk-factor is related to the outcome and hence clustered heterogeneity is interesting to investigate as the identity of the genetic variants in the clusters may reveal information about the risk factor and how it relates to the outcome
feature list: operation 3432
feature list: operation 3659
feature list: operation 3791

MR-MEGA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic 3517
citation: ddx280
citation: pmcid:PMC5755684
citation: pubmed:28911207
description: MR-MEGA (Meta-Regression of Multi-Ethnic Genetic Association) - tool to detect and fine-map complex trait association signals via trans-ethnic meta-regression.
feature list: operation_0487
feature list: operation_0488
feature list: operation 3197
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software version: beta 0.1.5
primary contact: Andrew P Morris
primary contact: Reedik Magi

MRICloud
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3304
application sub category: topic 3384
application sub category: topic 3444
citation: JON.12623
citation: pmcid:PMC6609486
citation: pubmed:31037800
description: Multi‐Atlas Label Fusion Tool for Neonatal Brain MRI Parcellation and Quantification.
feature list: operation 3799
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: login mricloud.html
primary contact: Kenichi Oishi
primary contact: Kumiko Oishi

MRIcron
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3334
application sub category: topic 3384
application sub category: topic 3422
application sub category: topic 3444
application sub category: topic 3452
citation: INJ.1836256.128
citation: pmcid:PMC6790816
citation: pubmed:31607099
description: Neural Correlates of Urinary Retention in Lateral Medullary Infarction. MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics. MRIcron is a mature and useful tool, however you may want to consider the more recent MRIcroGL as an alternative.
feature list: operation_0337
feature list: operation 3435

MRPrimerW2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0632
application sub category: topic 3512
application sub category: topic 3519
citation: GKZ323
citation: pmcid:PMC6602510
citation: pubmed:31045205
description: Tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments.
feature list: operation_0308
feature list: operation_0484
feature list: operation 3237
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
software help: helpSec
primary contact: https://orcid.org/0000-0003-4962-8272
primary contact: Min-Soo Kim

MRUniNovo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3520
application sub category: topic 3673
citation: btw721
citation: pubmed:27993788
description: Tool for de novo peptide sequencing utilizing the hadoop distributed computing framework.
feature list: operation_0476
feature list: operation 3202
feature list: operation 3644
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Kenli Li
primary contact: Tao Chen

MRtrix3
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0092
application sub category: topic 3384
application sub category: topic 3444
citation: J.NEUROIMAGE.2019.116137
citation: pubmed:31473352
description: A fast, flexible and open software framework for medical image processing and visualisation | MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualisation, with a particular emphasis on the investigation of the brain using diffusion MRI. It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational performance and a consistent command-line interface between applications. In this article, we provide a high-level overview of the features of the MRtrix3 framework and general-purpose image processing applications provided with the software
feature list: operation_0337
feature list: operation 3443

MS-Helios
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: s12859-018-2564-9
citation: pmcid:PMC6330434
citation: pubmed:30634897
description: Tool with multiple built-in data processing functions, allowing non-expert users to construct circular proteome maps (CPMs) or in general terms circular plots with a non-genomic basis.
feature list: operation_0417
feature list: operation 2939
feature list: operation 2940
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.1.8
primary contact: Harald Marx

MS2CNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3474
application sub category: topic 3520
citation: S12864-019-6297-6
citation: pmcid:PMC6929458
citation: pubmed:31874640
description: Predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks. Under construction, we will update it soon. MS2CNN compilation requires the following tools installed on your system Python, Keras==2.0.4 and Tensorflow==1.1.0. Predicting MS/MS spectrum based on protein sequence by Deep Convolutional Neural Networks. Lin YM, Chen CT, Chang JM. MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks. BMC Genomics. 2019;20(Suppl 9):906
feature list: operation 3643
feature list: operation 3646
feature list: operation 3767
feature list: operation 3801
feature list: operation 3860
license: GPL-3.0

MS2PIP Server
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic_0121
citation: btt544
citation: gkv542
citation: gkz299
citation: pmcid:PMC4489309
citation: pmcid:PMC5994937
citation: pmcid:PMC6602496
citation: pubmed:24078703
citation: pubmed:25990723
citation: pubmed:31028400
description: MS²PIP is a tool to predict MS² peak intensities from peptide sequences. This makes it possible to generate in silico predicted spectral libraries for full proteomes. MS²PIP employs the XGBoost machine learning algorithm and is written in Python.
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: howto
software help: api

MSDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0621
application sub category: topic 2885
application sub category: topic 3305
application sub category: topic 3489
citation: gkz886
citation: pmcid:PMC6943038
citation: pubmed:31599331
description: A comprehensive, annotated database of microsatellites. Multiple Loci VNTR Analysis databases and software. Multi Locus VNTR Analysis (MLVA) databases and software. MICAS 3.0, Microsatellite Analysis Server is the online repository of All Bacterial Microsatellites. MICAS: Microsatellite Analysis Server 3.0. An Online Repository of All Prokaryotic Microsatellites. with a focus on Viruses of Microbes and Molecular Epidemiology of bacterial pathogens. CRISPRCasdb: database for CRISPRs and associated Cas genes. MICAS: Microsatellite Analysis Server.
feature list: operation_0237
feature list: operation_0337
feature list: operation_0543
feature list: operation 3840

MSDRP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 2229
application sub category: topic 2640
application sub category: topic 3373
application sub category: topic 3676
citation: C9MO00162J
citation: pubmed:31802092
description: Modular within and between score for drug response prediction in cancer cell lines. Drug response prediction in cancer cell lines is vital to discover new anticancer drugs. However, it's still a challenging task to accurately predict drug responses in cancer cell lines. In this study, we presented a novel computational approach, named as MSDRP (modular within and between score for drug response prediction), to predict drug responses in cell lines. The method is based on a constructed heterogeneous drug-cell line network with multiple information. Compared with other state-of-the-art methods, MSDRP acquired better predictive performance, and identified potential associations between drugs and cell lines, which have been confirmed by the published literature. The source code of MSDRP is freely available at https: github.com shimingwang1994 MSDRP.git
feature list: operation 2495
feature list: operation 3439

MSIdV
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3682
output: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3591
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3360
application sub category: topic 3382
application sub category: topic 3520
citation: btw548
citation: pubmed:27542771
description: Tool to visualize biological indices from mass spectrometry imaging data.
feature list: operation_0337
feature list: operation 3627
feature list: operation 3860
is accessible for free: true
license: Unlicense
operating system: Windows
primary contact: Eisuke Hayakawa

MSIpred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2885
application sub category: topic 3295
application sub category: topic 3676
citation: s41598-018-35682-z
citation: pmcid:PMC6277498
citation: pubmed:30510242
description: Python package for tumor microsatellite instability classification from tumor mutation annotation data using a support vector machine.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md

MSMS-Chooser
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0769
application sub category: topic 3077
application sub category: topic 3520
citation: https://doi.org/10.1101/804401
description: Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure. Computational Selection of MSMS to Include in Library (MSMS-Chooser). Open-source Protocol for Community-created Public MS/MS Reference Library (MSMS-Chooser). MSMS-Chooser is a GNPS workflow and open-source protocol to empower the community to collect MS/MS reference data and contribute to the public MS/MS reference library.
feature list: operation 3644
feature list: operation 3646
feature list: operation 3860

MTBGT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0632
application sub category: topic 2885
application sub category: topic 3673
citation: https://doi.org/10.1101/628099
description: MTB Genome to Test (MTBGT) tool transforms WGS-derived data into laboratory-validated results of the primary RDTs – Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II.
feature list: operation 1812
feature list: operation 3196
feature list: operation 3435
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

MTGO-SC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3360
citation: FGENE.2019.00953
citation: pmcid:PMC6794379
citation: pubmed:31649730
description: Tool to Explore Gene Modules in Single-Cell RNA Sequencing Data. MTGO applied to Single Cell analysis. MTGO analysis applied to Single Cell data version 0.2.0 from GitHub. MTGO-SC is an adaptation for single cell RNA-sequencing (scRNA-seq) of MTGO, a biological network module detection algorithm. MTGO-SC integrates external gene annotations, such as the Gene Ontology terms or Reactome pathways with the gene expression networks obtained from single-cell DGE matrices. This package integrates MTGO (Module detection via Topological information and Gene Ontology (GO) knowledge) to single cell analysis. Effort is made to seamless integration of Seurat results, together with visualization and filtering functions. ne1s0n/MTGOsc: MTGO analysis applied to Single Cell data. Extracting gene modules from single cell RNA-seq cell clusters
feature list: operation_0277
feature list: operation 3083
feature list: operation 3432
feature list: operation 3463
license: GPL-3.0

MTK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0202
application sub category: topic_0749
application sub category: topic_0781
application sub category: topic 3297
citation: ACSSYNBIO.9B00322
citation: pubmed:31686495
description: A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells. Code and sequence files used in MTK manuscript
feature list: operation_0308
feature list: operation_0310

MTMR-Net
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
citation: TMI.2019.2934577
citation: pubmed:31403410
description: Multi-Task Deep Model with Margin Ranking Loss for Lung Nodule Analysis | Code for 《Multi-Task Deep Learning with Margin Ranking Loss for Lung Nodule Analysis》 | This is the pytorch implementation for 《MTMR-Net: Multi-Task Deep Learning with Margin Ranking Loss for Lung Nodule Analysis》 | Code for 《Multi-Task Deep Learning with Margin Ranking Loss for Lung Nodule Analysis》 Project
feature list: operation 3659

MTiAutoDock
type: SoftwareApplication
input: Small molecule structure
  type: FormalParameter
  additional type: data 1463
  encoding format: format 3814
  encoding format: format 3816
input: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1476
  encoding format: format 3816
output: Protein-ligand complex
  type: FormalParameter
  additional type: data 1461
  encoding format: format 1476
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3534
citation: gkv306
citation: pmcid:PMC4489289
citation: pubmed:25855812
description: Docking into a user-defined binding site or blind docking using AutoDock 4.2.
feature list: operation_0482
is accessible for free: true
license: Freeware
software help: MTiOpenScreen
software version: 1.0
primary contact: Maria A. Miteva

MTiOpenScreen
type: SoftwareApplication
input: Small molecule structure
  type: FormalParameter
  additional type: data 1463
  encoding format: format 3814
  encoding format: format 3816
input: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1476
  encoding format: format 3816
output: Protein-ligand complex
  type: FormalParameter
  additional type: data 1461
  encoding format: format 1476
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3343
citation: gkv306
citation: ijms20184648
citation: pmcid:PMC4489289
citation: pmcid:PMC6769597
citation: pubmed:25855812
citation: pubmed:31546814
description: Automated virtual screening with AutoDock Vina.
feature list: operation 3938
is accessible for free: true
license: Freeware
software help: MTiOpenScreen
software version: 1.0

MVApp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic_0780
citation: PP.19.00235
citation: pubmed:31061104
description: Multivariate analysis application for streamlined data analysis and curation.
feature list: operation 2939
feature list: operation 3659
feature list: operation 3891
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: MVApp
primary contact: Magdalena Julkowska

MVIAm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2269
application sub category: topic 3360
application sub category: topic 3518
citation: S41598-019-49967-4
citation: pmcid:PMC6751173
citation: pubmed:31534156
description: Multi-view based integrative analysis of gene expression data for identifying biomarkers | This repository provides some codes for this paper | The widespread applications in microarray technology have produced the vast quantity of publicly available gene expression datasets | If you are interested in it but have doubts about the content, please feel free to contact me | Communication: yangziyi091100@163.com
feature list: operation 2495
feature list: operation 3436

MWI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0593
application sub category: topic_0634
application sub category: topic 3444
citation: JON.12659
citation: pubmed:31407400
description: Myelin Water Fraction and Intra/Extracellular Water Geometric Mean T2 Normative Atlases for the Cervical Spinal Cord from 3T MRI | Normative atlases for the spinal cord using myelin water imaging | Myelin water imaging was applied in 20 healthy spinal cords to create T2 metric healthy population atlases that depict the mean and variation of myelin water fraction (MWF), and intra- and extra-cellular water mobility as described by geometric mean T2 (IEGMT2). The created atlases demonstrated structural variations in the spinal cord consistent with well-known anatomical characteristics. These atlases (in PAM50 space from Spinal Cord toolbox) can be used as a reference to demonstrate areas of abnormalities in individuals with myelin-related disease and damage. A full description of this work can be found in this paper: https://www.ncbi.nlm.nih.gov/pubmed/31407400
feature list: operation 3501
feature list: operation 3799

MaCProQC
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3712
output: Plot
  type: FormalParameter
  additional type: data 2884
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: biom13030491
citation: pmcid:PMC10046854
citation: pubmed:36979426
description: A workflow for the quality assessment of mass spectrometry (MS) based proteomics analyses
feature list: operation 3214
software version: 1

MaGenDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0622
application sub category: topic_0659
application sub category: topic_0769
application sub category: topic_0780
application sub category: topic 3512
citation: gkz953
citation: pmcid:PMC7145696
citation: pubmed:31665439
description: A functional genomics hub for Malvaceae plants. Pipelines of data analysis for MaGenDB
feature list: operation_0308
feature list: operation 2422
feature list: operation 2495
license: GPL-3.0

MaSIF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0166
application sub category: topic 2275
application sub category: topic 3172
application sub category: topic 3474
citation: S41592-019-0666-6
citation: pubmed:31819266
description: Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning. MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces. MaSIF- Molecular Surface Interaction Fingerprints: Geometric deep learning to decipher patterns in protein molecular surfaces. MaSIF is a proof-of-concept method to decipher patterns in protein surfaces important for specific biomolecular interactions
feature list: operation 2492
feature list: operation 2929
feature list: operation 3092
license: Apache-2.0

Mabellini
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0821
application sub category: topic 3421
citation: BAZ113
citation: pmcid:PMC6853642
citation: pubmed:31681953
description: A genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. An on-line source for Mycobacterium abscessus modeled structural proteome. MabeLLINI (Mycobacterium ABscessus modELLing INItiative) is a database available to anyone that wishes to know in detail the structural proteome of Mycobacterium abscessus. It contains thousands of models, generated with an unique domain-based methodology and thoroughly annotated with information from UniProt, CATH, SCOP and many more resources. These models are readily available for download, either individually or in bundles. To access them, simply use one of the many available queries or explore the data using our hierarchical interactive sunbursts
feature list: operation_0224
feature list: operation_0337
feature list: operation_0477
feature list: operation_0478

MaizeDIG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic_0625
application sub category: topic 3382
citation: FPLS.2019.01050
citation: pmcid:PMC6724615
citation: pubmed:31555312
description: Maize Database of Images and Genomes | MaizeDIG - Maize Database of Images and Genomes. This tool allows users to tag phenotypes in images and link them to specific genes | MaizeDIG the Maize Database of Images and Genomes, a genotypic-phenotypic database, for maize based on BioDIG | There are some prerequisites to set up MaizeDIG system such as installation of Django framework, Database system, Python and related libraries, and other dependencies | The Maize Genetics Executive Committee is reaching out to the global maize genetics, genomics, and breeding research communities to encourage researchers to become a maize cooperator (What is a maize cooperator?) Regions currently underrepresented within the maize cooperators are Africa, Asia, Europe, and Latin America
feature list: operation_0282
feature list: operation 3232
feature list: operation 3553

MaizeMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: An integrated data warehouse for MaizeGDB
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 1.3

MaizeSNPDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3293
application sub category: topic 3489
citation: J.CSBJ.2019.10.003
citation: pmcid:PMC6861670
citation: pubmed:31762961
description: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines. This R script chara-2-sparse.R is used to convert a traditional character genotype matrix into an integer sparse genotype matrix. This R script can be used in the system command line with R installed in the system or be used in the R enviroment. test.snp.RData is the input data to this R script. test.snp.RData is an R data file contained the genotype data of 1210 maize lines across 1000 SNP sites in character matrix. The content of this R data can be viewed in the R enviroment as shown below. MaizeSNPDB is deployed at http://150.109.59.144:3838/MaizeSNPDB/ for online use. The genotypes of 1210 maize lines at 35,370,939 SNP sites are stored using Sparse Matrices in R. MaizeSNPDB is idle until you activate it by accessing the URL. After running the R script, a new R data file named as test.snp. Mat.
feature list: operation_0282
feature list: operation 2422
feature list: operation 3196
feature list: operation 3431

Making Soup
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0176
application sub category: topic_0593
application sub category: topic 3047
application sub category: topic 3292
application sub category: topic 3306
citation: CHEMRXIV.10102289.V1
description: Preparing and Validating Molecular Simulations of the Bacterial Cytoplasm. The cytoplasm of a cell is sometimes jestingly called a Soup, since it contains many different ingredients. Indeed there is quite a bit of salt and glutamate, the well known flavour enhancing compoud that is used a lot in asian kitchen but also in broth. Read more here: https://en.wikipedia.org/wiki/Glutamate_flavoring. In order to study the cytoplasm of a cell one can use a variety of experimental biochemistry techniques, but also computer simulations, which is the focus of this page. Here we thererfore provide information and python scripts to run computer simulations using http://www.gromacs.org of (quite) realistic models of the cytoplasm. The main work is done here by a few scripts, located in the aptly named scripts directory. They are described briefly in the README.md in that directory
feature list: operation_0480
feature list: operation 2476
feature list: operation 3891

MalariaGEN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3305
application sub category: topic 3518
citation: https://doi.org/10.1101/824730
description: An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Plasmodium falciparum Community Project. Dried blood spot collection. Photo credit: Will Hamilton. HiSeq machines at the Wellcome Trust Sanger Institute. Photo credit: Genome Research Limited. We're working with researchers in malaria-endemic countries to generate large-scale genetic and genomic data on all three malaria genomes: human, parasite, and mosquito. The Plasmodium falciparum Community Project supports groups around the world to integrate parasite genome sequencing into clinical and epidemiological studies of malaria. Our projects provide a framework for malaria researchers around the world to work together on large-scale studies that combine epidemiology with the analysis of genome variation to better understand the evolutionary battle between human hosts, malaria parasites, and the mosquito vector
feature list: operation_0484
feature list: operation 3196
feature list: operation 3211
feature list: operation 3629
feature list: operation 3891

Malaria Data District
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3063
application sub category: topic 3305
citation: WELLCOMEOPENRES.15495.1
description: An open-source web application for increasing access to malaria information. Preventable diseases still cause huge mortality in low- and middle-income countries. Research in spatial epidemiology and earth observation is helping academics to understand and prioritise how mortality could be reduced and generates spatial data that are used at a global and national level, to inform disease control policy. These data could also inform operational decision making at a more local level, for example to help officials target efforts at a local regional level. To be usable for local decision-making, data needs to be presented in a way that is relevant to and understandable by local decision makers. We demonstrate an approach and prototype web application to make spatial outputs from disease modelling more useful for local decision making.
feature list: operation_0337

Manhattan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 2885
application sub category: topic 3500
application sub category: topic 3517
citation: S12859-019-3201-Y
citation: pmcid:PMC6882345
citation: pubmed:31775616
description: Displaying genome-wide association summary statistics with multiple annotation layers. A useful way to summarize genome-wide association data is with a Manhattan plot. This type of plot has a point for every SNP or location tested with the position in the genome along the x-axis and the -log10 p-value on the y-axis
feature list: operation_0337
feature list: operation 3359
feature list: operation 3661

Manhattan Harvester
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3517
citation: s12859-019-2600-4
citation: pmcid:PMC6330393
citation: pubmed:30634901
description: Tool for automatically detecting and characterizing peaks from GWAS output files (Manhattan Plots).
feature list: operation 3215
feature list: operation 3222
feature list: operation 3557
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: T. Haller

MapCaller
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic 3168
citation: https://doi.org/10.1101/783605
description: MapCaller – An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data | MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes | MapCaller: An efficient and versatile approach for short-read mapping and variant identification using high-throughput sequenced data | MapCaller aligns every NGS short read against a reference genome and collects all the alignment information to deduce sequence variants
feature list: operation_0452
feature list: operation 3198
feature list: operation 3227
license: MIT

MapOptics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 3382
citation: bty1013
description: Lightweight cross-platform tool that enables the user to visualise and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid scaffolding alignments.
feature list: operation_0337
feature list: operation 1812
feature list: operation 3216
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Fady Mohareb

MapStore
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0621
application sub category: topic 3263
application sub category: topic 3489
citation: PEERJ.PREPRINTS.2247V2
description: The opendata geoportal of the Lamma Consortium.
feature list: operation 3454
feature list: operation 3695
license: CC-BY-4.0

Mapper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3067
application sub category: topic 3304
citation: NETN A 00094
citation: pmcid:PMC6663211
citation: pubmed:31410377
description: Topological gene expression networks recapitulate brain anatomy and function | Code for reproducing results in the paper "Topological gene-expression networks recapitulate brain anatomy and function" | TDA summary for gene-expression: Mapper Algorithm in 2D | Understanding how gene expression translates to and affects human behaviour is one of the ultimate aims of neuroscience
feature list: operation 3463
feature list: operation 3562
feature list: operation 3766

MariaOsmala
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3179
application sub category: topic 3295
application sub category: topic 3474
citation: https://doi.org/10.1101/804625
description: Enhancer prediction in the human genome by probabilistic modeling of the chromatin feature patterns. This package is a PRobabilistic Enhancer PredictIoN Tool PREPRINT. Clone the project to the desired directory, this will be your path_to_dir. https://github.com/MariaOsmala/RFECS_BUG_FIXES.git.
feature list: operation_0440
feature list: operation_0441
feature list: operation 2575
license: MIT

MarkerHub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0218
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3474
citation: bax082
citation: pmcid:PMC7243925
citation: pubmed:31725857
description: Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy. We aimed to design a hybrid system for systematic entity recognition and ranking to identify poten-tial biomarkers for liver cancer
feature list: operation_0305
feature list: operation 2422
feature list: operation 3280

Mascot Daemon
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
description: Mascot Daemon is a Microsoft Windows client application that automates the submission of data files to Mascot server.
feature list: operation 3762
feature list: operation 3763
is accessible for free: true
license: Proprietary
operating system: Windows

Mascot Distiller
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 2330
  encoding format: format 3244
  encoding format: format 3654
  encoding format: format 3710
  encoding format: format 3712
  encoding format: format 3858
output: Protein report
  type: FormalParameter
  additional type: data_0896
  encoding format: format 2331
  encoding format: format 2332
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3651
  encoding format: format 3652
  encoding format: format 3834
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
description: Mascot Distiller Workstation offers a single, intuitive interface to a wide range of native (binary) mass spectrometry data files. A unique algorithm, which fits each peak to a calculated isotope distribution, processes the raw data into high quality, de-isotoped peak lists. This core functionality can be extended by adding one or more toolboxes. These are optional collections of tools for specific tasks, such as Mascot search result review, automatic and manual de novo sequencing, quantitation, and batch processing. There is also a developer’s package that provides access to the API of the underlying COM library.
feature list: operation 3215
feature list: operation 3629
feature list: operation 3634
feature list: operation 3635
feature list: operation 3643
feature list: operation 3644
feature list: operation 3646
is accessible for free: false
license: Proprietary
operating system: Windows

Mascot Parser
type: SoftwareApplication
input: Database search results
  type: FormalParameter
  additional type: data 2080
  encoding format: format 3713
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0121
description: Mascot Parser provides an object-oriented Application Programmer Interface (API) to Mascot result files and configuration files, making it easy for programs written in C++, C#, Java, Perl or Python to access Mascot results.
feature list: operation 1812
is accessible for free: true
license: Proprietary
operating system: Linux
operating system: Windows
software help: help

Mass Spec Studio
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic_0769
application sub category: topic 2814
application sub category: topic 3520
citation: j.str.2014.08.013
citation: acs.analchem.9b01625
citation: mcp.O116.058685
citation: pmcid:PMC4391204
citation: pmcid:PMC5013318
citation: pubmed:25242457
citation: pubmed:27412762
citation: pubmed:31198032
description: An extensible, vendor-agnostic application for mass spectrometry analysis. Current analysis packages include protein-protein crosslinking (XL), hydrogen/deuterium exchange (HX), covalent labelling quantification and normalization (CLEAN).
feature list: operation_0321
feature list: operation 2409
feature list: operation 2492
feature list: operation 3694
is accessible for free: true
license: Apache-2.0
operating system: Windows
software help: MSStudio-XL-tutorial-1.pdf
software version: 2.3.0

MasterMSM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic_0602
citation: ACS.JCIM.9B00468
citation: pubmed:31423789
description: A Package for Constructing Master Equation Models of Molecular Dynamics | Python package for generating Markov state models | MasterMSM is a Python package for generating Markov state models (MSMs) from molecular dynamics trajectories. We use a formulation based on the chemical master equation. This package will allow you to:
feature list: operation_0244
feature list: operation 2476
license: GPL-2.0

MasterOfPores
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 3047
application sub category: topic 3170
application sub category: topic 3316
application sub category: topic 3512
citation: https://doi.org/10.1101/818336
description: Parallel and scalable workflow for the analysis of Oxford Nanopore direct RNA sequencing datasets. Nextflow pipeline for analysis of Nanopore reads (from RNA/cDNA/DNA). Please read the documentation here: https://biocorecrg.github.io/master_of_pores/. Nextflow pipeline for analysis of Nanopore data from direct RNA sequencing. This is a joint project between CRG bioinformatics core and Epitranscriptomics and RNA Dynamics research group.
feature list: operation_0428
feature list: operation 3185
feature list: operation 3218
license: MIT

Mat_Peptide
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 3324
application sub category: topic 3400
citation: btz777
citation: pmcid:PMC8215913
citation: pubmed:31609421
description: Comprehensive annotation of mature peptides from polyproteins in five virus families. Annotate a viral polyprotein by projecting reference mature peptide annotation through global alignment. The United States Government Department of Health and Human Services, National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases, owns the copyright to the accompanying software under FAR 52.227-14 (c).
feature list: operation_0491
feature list: operation_0496
feature list: operation 2421
license: MIT

Matched Forest
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0091
application sub category: topic 3474
citation: BTZ785
citation: pubmed:31621830
description: Supervised Learning for High-dimensional Matched Case-Control Studies. This code implements Matched Forest algorithm which aims to find important variables in high-dimensional matched case-control data sets. Please refer to our papers for more details:
feature list: operation 2940
feature list: operation 3659

MathIOmica
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic 3170
application sub category: topic 3172
application sub category: topic 3308
application sub category: topic 3577
citation: cpbi.91
citation: pmcid:PMC8686519
citation: pubmed:31851777
description: General Analysis Utilities for Dynamic Omics Datasets. MathIOmica is a package for bioinformatics, written in the Wolfram language, that provides multiple utilities to facilitate the analysis of longitudinal data generated from omics experiments, including transcriptomics, proteomics, and metabolomics data, as well as any generalized time series. MathIOmica uses Mathematica's notebook interface, wherein users can import longitudinal datasets, carry out quality control and normalization, generate time series, and classify temporal trends. MathIOmica provides spectral methods based on periodograms and autocorrelations for automatically detecting classes of temporal behavior and allowing the user to visualize collective temporal behavior, and also assess biological significance through Gene Ontology and pathway enrichment analyses. MathIOmica's time-series classification methods address common issues including missing data and uneven sampling in measurements.
feature list: operation 3083
feature list: operation 3435
feature list: operation 3565

MatrisomeDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0621
application sub category: topic 2640
application sub category: topic 3520
citation: GKZ849
citation: pubmed:31586405
description: The ECM-protein knowledge database.
feature list: operation_0417
feature list: operation 2421
feature list: operation 2422
feature list: operation 3216
feature list: operation 3431
feature list: operation 3755
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

MatrixMotif
type: SoftwareApplication
input: Sequence trace
  type: FormalParameter
  additional type: data_0924
  encoding format: format 1929
output: Position weight matrix
  type: FormalParameter
  additional type: data 1362
  encoding format: format 2064
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Script
additional type: Workflow
application sub category: topic_0085
application sub category: topic_0749
author: https://orcid.org/0000-0002-3036-4345
description: We propose MatrixMotif(MM), a new combinatorial hybrid algorithm allowing qualitative and quantitative analysis of TFBS (Transcription Factor Binding Site) motifs using NGS data originated from DNA extraction and enrichment techniques. MM allows de novo motifs discovery and motifs iteration employing enumerative and probabilistic models based on several types of matrixes. MM primarily utilizes set of sequences from NGS in fasta format as a template for mathematical and statistical modeling. Fasta format can be generated from fastq format (Illumina platform) set of individual enriched sequences. MM generates final motifs as PPM, PWM or TFFM allowing visualization of de novo computed motifs.
feature list: operation_0234
feature list: operation_0238
feature list: operation_0239
feature list: operation_0364
feature list: operation 3472
is accessible for free: true
license: GPL-3.0
operating system: Linux
software version: 1.0
primary contact: https://orcid.org/0000-0002-3036-4345

MaveDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0749
application sub category: topic 3168
application sub category: topic 3577
citation: S13059-019-1845-6
citation: pmcid:PMC6827219
citation: pubmed:31679514
description: An open-source platform to distribute and interpret data from multiplexed assays of variant effect. Table of Multiplexed Assay of Variant Effect (MAVE) studies. MaveDB - A repository for MAVE assay datasets. To cite this document, please use the citation details for MaveDB. MaveDB is a public repository for datasets from Multiplexed Assays of Variant Effect (MAVEs), such as those generated by deep mutational scanning (DMS) or massively parallel reporter assay (MPRA) experiments. Welcome to our table of Multiplexed Assay of Variant Effect (MAVE) studies. To contribute a study or amend/expand an existing entry, please use the GitHub issue tracker or create a pull request
feature list: operation_0337
feature list: operation 2422
feature list: operation 3227
feature list: operation 3431
license: CC-BY-4.0

MeLAD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic 3489
citation: BTZ648
citation: pubmed:31504189
description: An integrated resource for metalloenzyme-ligand associations | The Metalloenzyme-Ligand Association Database (MeLAD)
feature list: operation_0482
feature list: operation 3501
feature list: operation 3898

Mecan4CNA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0632
application sub category: topic 2885
application sub category: topic 3518
citation: https://doi.org/10.1101/720854
description: Minimum Error Calibration and Normalization for Genomic Copy Number Analysis | Minimum Error Calibration and Normalization for Copy Number Analysis | A copy number profile usually needs to be calibrated for the position of baseline (normal copy numbers) due to sample impurity and measurement bias. It’s crucial to normalize CN profiles when comparing them in analysis, because usually each profile has a different signal scale | Mecan4CNA (Minimum Error Calibration and Normalization for Copy Number Analysis) uses an algebraic method to estimate the baseline and the distance between DNA levels (referred to as level distance). It can be used for both single file analysis and multi-file normalization | A copy number profile usually needs to be calibrated for the position of baseline (normal copy numbers) due to sample impurity and measurement bias. It's crucial to normalize CN profiles when comparing them in analysis, because usually each profile has a different signal scale
feature list: operation 3196
feature list: operation 3233
feature list: operation 3435
license: MIT

MechSpy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2840
application sub category: topic 3292
application sub category: topic 3378
citation: https://doi.org/10.1101/782011
description: Applying knowledge-driven mechanistic inference to toxicogenomics | Mechanistic inference of toxicity from gene expression time series and knowledge graphs | Mechanistic inference for toxicology | This repository provide the code for the publication "Applying knowledge-driven mechanistic inference to toxicogenomics" (DOI: xxxxxxxxxxxx) and contains the collection of scripts to reproduce the results obtained. Besides the code, this repository provides: | $ git clone git@github.com:ignaciot/MechSpy.git | You can add new mechanisms of your own to MechSpy by editing mechanisms.py. A mock, commented-out "M12" mechanism was added to illustrate where would new mechanisms need to go
feature list: operation 3501
feature list: operation 3642
license: MIT

MedicMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: MedicMine integrates many types of data for Medicago truncatula. You can run flexible queries, export results and analyse lists of genes.
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 1.3.0

Meffil
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3173
application sub category: topic 3295
citation: pmcid:PMC6247925
citation: pubmed:29931280
description: algorithms for analyzing DNA methylation data generated using Infinium HumanMethylation450 or MethylationEPIC BeadChips Epigenome-Wide Association Studies (EWAS)
feature list: operation 1812
feature list: operation 3196
is accessible for free: true
license: Artistic-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: readme.md
primary contact: Matthew Suderman

MegaGTA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3293
application sub category: topic 3697
application sub category: topic 3837
citation: FGENE.2019.00957
citation: pmcid:PMC6843070
citation: pubmed:31749830
description: Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes. HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs. git clone https://github.com/HKU-BAL/megagta.git.
feature list: operation_0523
feature list: operation_0524
feature list: operation_0525
feature list: operation 3192
feature list: operation 3731

Meltos
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic 3175
application sub category: topic 3673
citation: btz737
citation: pmcid:PMC8215921
citation: pubmed:31584621
description: Multi-Sample Tumor Phylogeny Reconstruction for Structural Variants. Meltos is a novel approach to estimate the variant allele frequency of somatic SVs from whole genome sequencing (WGS) signals and using these VAFs to identify the phylogenetic relationship between SSVs in a multi-sample cell lineage tree using an SNV-only tree as a basis. Our probabilistic framework allows us to assess multiple types of signals taken from the data simultaneously and more accurately calculate the VAF of SV events. Following the maximum parsimony principle, Meltos uses a novel combinatorial algorithm to assign SV clusters on the branches of the given lineage tree, while modestly augmenting the tree topology if needed
feature list: operation 3216
feature list: operation 3227
feature list: operation 3233
feature list: operation 3478
license: MIT

MemSurfer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0153
application sub category: topic_0820
application sub category: topic 3306
citation: ACS.JCTC.9B00453
citation: pubmed:31564100
description: A Tool for Robust Computation and Characterization of Curved Membranes | MemSurfer is a software tool to compute bilayer membrane surfaces | Biochemical and Biophysical Systems Group | MemSurfer is an efficient and versatile tool to compute and analyze membrane surfaces found in a wide variety of large-scale molecular simulations | Advances in simulation methodologies, code efficiency, and computing power have enabled larger, longer, and more-complicated biological membrane simulations
license: GPL-3.0

MeroX
type: SoftwareApplication
input: Mass spectrometry spectra
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3244
  encoding format: format 3651
input: Protein sequence record
  type: FormalParameter
  additional type: data 2886
  encoding format: format 1929
output: Data
  type: FormalParameter
  additional type: data_0006
  encoding format: format 1915
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic 1317
author: https://orcid.org/0000-0003-4001-2324
citation: s13361-011-0261-2
citation: s13361-014-1001-1
citation: acs.analchem.5b04853
citation: s41596-018-0068-8
citation: pubmed:22038510
citation: pubmed:25261217
citation: pubmed:27428000
citation: pubmed:30382245
description: Analysis tool for protein-protein cross-linking using MS-cleavable cross-lining reagents such as DSBU, DSSO, CDI or PIR linker
feature list: operation_0004
is accessible for free: true
license: Freeware
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.htm
software version: 2.0 (2.0.0.7)

MetAML
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
citation: journal.pcbi.1004977
citation: pmcid:PMC4939962
citation: pubmed:27400279
description: Computational tool for metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. The tool (i) is based on machine learning classifiers, (ii) includes automatic model and feature selection steps, (iii) comprises cross-validation and cross-study analysis, and (iv) uses as features quantitative microbiome profiles including species-level relative abundances and presence of strain-specific markers. It provides also species-level taxonomic profiles, marker presence data, and metadata for 3000+ public available metagenomes.
software help: wiki
software version: 1.0

MetGem
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3172
application sub category: topic 3520
citation: ACS.ANALCHEM.9B02802
citation: pubmed:31429549
description: Generation of a Molecular Network from Electron Ionization Mass Spectrometry Data by Combining MZmine2 and MetGem Software | Calculation and visualization of molecular networks based on t-SNE algorithm - metgem/metgem | MetGem is an open-source software for tandem mass-spectrometry data visualization. It's key features are standalone molecular networking and t-SNE based projections
feature list: operation 3431
feature list: operation 3501
feature list: operation 3629

MetHis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3056
citation: https://doi.org/10.1101/761452
description: Complex genetic admixture histories reconstructed with Approximate Bayesian Computations | MetHis is a population genetics forward simulation tool designed to simulate arbitrarily complex admixture histories between two populations
feature list: operation_0487
feature list: operation 3196
feature list: operation 3891
license: GPL-3.0

MetPC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3360
citation: METABO9050103
citation: pmcid:PMC6572057
citation: pubmed:31130635
description: Metabolite Pipeline Consisting of Metabolite Identification and Biomarker Discovery Under the Control of Two-Dimensional FDR.
feature list: operation 3659
feature list: operation 3803
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Jaesik Jeong

MetWork
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3343
citation: ACS.ANALCHEM.9B02216
citation: pubmed:31369240
description: Computer-Assisted Natural Products Anticipation | a web server for natural products anticipation | Currently running beta version 0.4.2 | "Essence is a function of the relationship." Bachelard 1929 | MetWork used for the identification of bromotryptamine derivatives
feature list: operation 3627
feature list: operation 3629
feature list: operation 3803

Meta-4mCpred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0749
application sub category: topic 3295
application sub category: topic 3474
citation: J.OMTN.2019.04.019
citation: pmcid:PMC6540332
citation: pubmed:31146255
description: Sequence-Based Meta-Predictor for Accurate DNA 4mC Site Prediction Using Effective Feature Representation.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: 4mCPredtutorial.html
primary contact: Balachandran Manavalan
primary contact: Gwang Lee
primary contact: Leyi Wei

Meta-iAVP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3373
application sub category: topic 3379
application sub category: topic 3382
application sub category: topic 3474
citation: IJMS20225743
citation: pmcid:PMC6888698
citation: pubmed:31731751
description: A Sequence-Based Meta-Predictor for Improving the Prediction of Antiviral Peptides Using Effective Feature Representation. In spite of the large-scale production and widespread distribution of vaccines and antiviral drugs, viruses remain a prominent human disease. Recently, the discovery of antiviral peptides (AVPs) has become an influential antiviral agent due to their extraordinary advantages. With the avalanche of newly-found peptide sequences in the post-genomic era, there is a great demand to develop a sequence-based predictor for timely identifying AVPs as this information is very useful for both basic research and drug development. In this study, we propose a novel sequence-based meta-predictor with an effective feature representation, called Meta-iAVP, for the accurate prediction of AVPs from given peptide sequences. Herein, the effective feature representation was extracted from a set of prediction scores derived from various machine learning algorithms and types of features
feature list: operation_0252
feature list: operation 3436
feature list: operation 3631

MetaBAT 2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3837
citation: peerj.1165
citation: peerj.7359
citation: pmcid:PMC4556158
citation: pmcid:PMC6662567
citation: pubmed:26336640
citation: pubmed:31388474
description: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning
feature list: operation_0310
feature list: operation_0362
feature list: operation 3798

MetaCRAST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: PEERJ.PREPRINTS.2278V2
citation: pmcid:PMC5592083
citation: pubmed:28894651
description: Reference-guided extraction of CRISPR spacers from unassembled metagenomes. MetaCRAST: reference-guided CRISPR detection in metagenomes. MetaCRAST (Metagenomic CRISPR Reference-Aided Search Tool) is a tool to detect CRISPR arrays in raw, unassembled metagenomes. Unlike other tools, it uses expected CRISPR direct repeat (DR) sequences from assembled contigs or bacterial genomes to guide metagenomic CRISPR detection. It uses a fast implementation of the Wu-Manber multipattern search algorithm to rapidly select reads that contain an expected DR sequence. It then proceeds through reads identified in the previous step to find DR sequences within acceptable distances of each other (i.e., with acceptable length spacers between them). Spacers between these DRs are then extracted and clustered into a non-redundant set with CD-HIT
feature list: operation_0310
feature list: operation 2421
feature list: operation 3460
license: GPL-3.0

MetaCarvel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3837
citation: S13059-019-1791-3
citation: pmcid:PMC6710874
citation: pubmed:31451112
description: MetaCarvel: A scaffolder for metagenomes | MetaCarvel - Scaffolder for metagenomes | MetaCarvel is an updated version of previous metagenome scaffolder Bambus 2. To run MetaCarvel, you will need Python 2.7.x, Samtools, Bedtools, Networkx(Version < 1.11), NumPy,and OGDF
feature list: operation_0524
feature list: operation 2495
feature list: operation 3216
license: MIT

MetaCell
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: S13059-019-1812-2
citation: pmcid:PMC6790056
citation: pubmed:31604482
description: Analysis of single-cell RNA-seq data using K-nn graph partitions. scRNA-seq profiles each represent a highly partial sample of mRNA molecules from a unique cell that can never be resampled, and robust analysis must separate the sampling effect from biological variance. We describe a methodology for partitioning scRNA-seq datasets into metacells: disjoint and homogenous groups of profiles that could have been resampled from the same cell. Unlike clustering analysis, our algorithm specializes at obtaining granular as opposed to maximal groups. We show how to use metacells as building blocks for complex quantitative transcriptional maps while avoiding data smoothing. Our algorithms are implemented in the MetaCell R C++ software package.
feature list: operation 2495
feature list: operation 3432
feature list: operation 3799

MetaDEGalaxy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 3170
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: F1000RESEARCH.18866.2
citation: pmcid:PMC6807170
citation: pubmed:31737256
description: Galaxy workflow for differential abundance analysis of 16s metagenomic data. You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. This history is empty. You can load your own data or get data from an external source
feature list: operation_0232
feature list: operation 3219
feature list: operation 3435

MetaDome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic_0736
citation: humu.23798
citation: pmcid:PMC6772141
citation: pubmed:31116477
description: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains.
feature list: operation_0303
feature list: operation 3197
feature list: operation 3436
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: about

MetaErg
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0160
application sub category: topic_0602
application sub category: topic 3174
citation: FGENE.2019.00999
citation: pmcid:PMC6803454
citation: pubmed:31681429
description: An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. MetaErg is a stand-alone and fully automated metagenomic and metaproteomic data annotation pipeline. It bundles essential annotation tasks such as feature prediction, functional annotation with Hidden Markov Model (HMM) searches as well as blast and diamond searches. It estimates and visualizes quantitative taxonomic and pathway compositions of multiple metagenomic and proteomics samples using sequencing coverage and proteomics spectral counts, respectively. For visualization, MetaErg provides a HTML interface, bringing all annotation results together in sortable and searchable tables, collapsible trees, and other graphic representations, enabling intuitive navigation of complex data. Analysis statistics: master.stats.txt. Analysis annotation in gff format: master.gff.txt. MetaErg begins biological feature and element prediction by identifying CRISPR elements and non-coding RNA genes (tRNA, rRNA genes)
feature list: operation_0310
feature list: operation_0362
feature list: operation 3083
feature list: operation 3439
feature list: operation 3460

MetaEuk
type: SoftwareApplication
input: Sequence set (nucleic acid)
  type: FormalParameter
  additional type: data 1234
  encoding format: format 1929
output: Sequence set (protein)
  type: FormalParameter
  additional type: data 1233
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0623
application sub category: topic 3174
citation: https://doi.org/10.1101/851964
citation: s40168-020-00808-x
citation: pmcid:PMC7126354
citation: pubmed:32245390
description: MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
feature list: operation 3663
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software version: 1-ea903e5
software version: 2-ddf2742

MetaGxBreast
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic_0634
application sub category: topic 2640
author: Benjamin Haibe-Kains
author: Deena M.A. Gen-doo
description: A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium.
feature list: operation_0441
feature list: operation 2436
feature list: operation 3223
is accessible for free: true
license: Artistic-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: MetaGxBreast.pdf
primary contact: Benjamin Haibe-Kains
primary contact: Michael Zon

MetaMEx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic 3295
application sub category: topic 3308
application sub category: topic 3390
application sub category: topic 3407
citation: https://doi.org/10.1101/813048
description: Transcriptomic Profiling of Skeletal Muscle Adaptations to Exercise and Inactivity. Transcriptomics meta-analysis of skeletal muscle response to exercise. Transcriptomics meta-analysis of skeletal muscle response to exercise. The shiny app is available at www.metamex.eu.
feature list: operation 2495

MetaMed
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3174
application sub category: topic 3303
application sub category: topic 3697
citation: MSYSTEMS.00413-19
citation: pmcid:PMC6787565
citation: pubmed:31594829
description: Linking Microbiota Functions with Medicine Therapeutics. Metagenomics Medicine mapping system (MetaMed), is a novel and integrative system-wide correlation mapping system to link bacteria functions and medicine therapeutics
feature list: operation 3432
feature list: operation 3660
feature list: operation 3803

MetaMiner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 2229
application sub category: topic 3174
application sub category: topic 3520
application sub category: topic 3697
citation: j.cels.2019.09.004
citation: pmcid:PMC6952069
citation: pubmed:31629686
description: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery.
feature list: operation 3755
feature list: operation 3803

MetaMorpheus
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3244
  encoding format: format 3651
  encoding format: format 3712
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
  encoding format: format 3770
output: Peptide identification
  type: FormalParameter
  additional type: data_0945
  encoding format: format 3247
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0601
application sub category: topic 3520
application sub category: topic 3922
citation: acs.jproteome.0c00838
citation: acs.jproteome.9b00330
citation: pmcid:PMC6733628
citation: pmcid:PMC8377504
citation: pubmed:31378069
citation: pubmed:33683901
description: Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data | Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities | MetaMorpheus: Free, Open-Source PTM Discovery | Download the current version here. For first-time Windows users, choose "MetaMorpheusInstaller.msi" and install MetaMorpheus. Check out our getting started video on YouTube
feature list: operation 2421
feature list: operation 3215
feature list: operation 3629
feature list: operation 3631
feature list: operation 3649
feature list: operation 3755
feature list: operation 3767
license: MIT

MetaOmics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0602
application sub category: topic_0769
application sub category: topic 3308
citation: bty825
citation: pmcid:PMC6499246
citation: pubmed:30304367
description: Analysis pipeline and browser-based software suite for transcriptomic meta-analysis.
feature list: operation 3463
feature list: operation 3501
feature list: operation 3766
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: metaOmics turtorial.pdf
software help: README.md

MetaQUBIC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
application sub category: topic 3308
application sub category: topic 3697
citation: btz414
citation: pmcid:PMC6821265
citation: pubmed:31116375
description: Integrated biclustering-based computational pipeline for gene module detection that integrates both metagenomic and metatranscriptomic data.
feature list: operation 2422
feature list: operation 2495
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
software help: issues
primary contact: Qin Ma

MetaR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic 3170
application sub category: topic 3372
application sub category: topic 3676
citation: PEERJ.PREPRINTS.1465V2
description: Simple, high-level languages for data analysis with the R ecosystem. Simple Data Analysis language built with MPS. Generates R code. Metaprogramming in R, thus the name. MetaR takes advantage of Language Workbench Technology to facilitate data analysis with the R language. It can be used by:. Apache Server at metar.campagnelab.org Port 80. bioinformaticians who wish to package state of the art analysis methods into user friendly metaR analysis language constructs. MetaR can act as a bridge between analysis experts who develop analysis methods in R and wish to distribute these methods to the broadest audience without investing a lot of effort in developing user interfaces.
feature list: operation_0555
feature list: operation 2422
feature list: operation 2495

MetaSanity
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0769
application sub category: topic 3382
application sub category: topic 3697
citation: https://doi.org/10.1101/789024
description: An integrated, customizable microbial genome evaluation and annotation pipeline. Pipeline for major biological analyses. MetaSanity v1.1.1 - 2020 version. MetaSanity v1.1.1 provides a unified workflow for genome assessment and functional annotation that combines all outputs into a single queryable database – all within an easily distributed Docker image
feature list: operation_0362
feature list: operation 2422
feature list: operation 2489
license: GPL-3.0

MetaSpark:
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 3174
application sub category: topic 3837
citation: btw750
citation: pubmed:28065898
description: Spark-based distributed processing tool to recruit metagenomic reads to reference genomes.
feature list: operation_0310
feature list: operation 2495
feature list: operation 3472
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Beifang Niu
primary contact: Jing Luo

MetaTOR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3697
citation: FGENE.2019.00753
citation: pmcid:PMC6710406
citation: pubmed:31481973
description: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries | Metagenomic binning based on Hi-C data | pip3 install -e git+https://github.com/koszullab/metator.git@master#egg=metator | Metagenomic Tridimensional Organisation-based Reassembly - A set of scripts that streamline the processing and binning of metagenomic 3C datasets | Please refer to the tutorial in order to quickly get the pipeline up and running on example data (or your own), and the metaTOR manual for detailed explanations on the parameters
feature list: operation_0310
feature list: operation 3192
feature list: operation 3798
license: GPL-3.0

MetaboList
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3520
citation: METABO9090187
citation: pmcid:PMC6780920
citation: pubmed:31533242
description: A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis | Annotation of Metabolites from Liquid Chromatography-Mass Spectrometry Data | Automatic metabolite annotation from Liquid Chromatography-Mass Spectrometry (LC-MS and LC-MS/MS DIA) analysis
feature list: operation 2495
feature list: operation 3803
license: GPL-2.0

MetaboPath View
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3172
description: Graphical visualization tool for metabolomics and genomic data within metabolic pathways
feature list: operation 3660

Metabolic Disassembler
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic_0769
application sub category: topic 3047
application sub category: topic 3407
citation: S12859-019-3183-9
citation: pmcid:PMC6929434
citation: pubmed:31870296
description: Metabolic disassembler for understanding and predicting the biosynthetic units of natural products. The Metabolic Disassembler is a Python package to automatically predict a combination of biosynthetic units in a natural product. This software would help to reveal the starting materials of the target natural product.
feature list: operation_0337
feature list: operation_0533
feature list: operation 3439
license: MIT

Metadata Editor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0219
description: FAIR metadata editor for guiding the user through the creation of FAIR Data Point metadata.
is accessible for free: true
license: MIT

Metage2Metabo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3172
application sub category: topic 3174
application sub category: topic 3407
citation: https://doi.org/10.1101/803056
description: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species. From annotated genomes to metabolic screening in large scale microbiotas. Metage2metabo is a Python3 (Python >= 3.6) tool to perform graph-based metabolic analysis starting from annotated genomes (reference genomes or metagenome-assembled genomes). It uses Pathway Tools in a automatic and parallel way to reconstruct metabolic networks for a large number of genomes. The obtained metabolic networks are then analyzed individually and collectively in order to get the added value of metabolic cooperation in microbiota over individual metabolism and to identify and screen interesting organisms among all. m2m — metage2metabo documentation. Free document hosting provided by Read the Docs
feature list: operation_0310
feature list: operation_0362
feature list: operation 3660
license: GPL-3.0
software help: metage2metabo.readthedocs.io

Metagenomic read binning using sparse coding
type: SoftwareApplication
input: Matrix
  type: FormalParameter
  additional type: data 2082
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
description: This code implements a pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in the field of metagenomics
feature list: operation 3798
is accessible for free: true
license: MIT
operating system: Linux

Metandem
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3520
citation: J.ACA.2019.08.046
citation: pmcid:PMC6814207
citation: pubmed:31623721
description: An online software tool for mass spectrometry-based isobaric labeling metabolomics. Metandem - A Data Analysis Tool for Isobaric Labeling-based Metabolomics. Metandem is a free online data analysis platform for mass spectrometry-based isobaric labeling metabolomics. It allows users to upload and process MS or hyphenated MS data files for isobaric-labeling-based quantitative and qualitative metabolomics analyses, including feature extraction, metabolite quantification, metabolite identification, batch processing of multiple data files, parameter optimization, median normalization, and statistical analysis. Results can be downloaded or visualized online
feature list: operation 3435
feature list: operation 3799
feature list: operation 3803

Metapop
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3056
citation: https://doi.org/10.1111/1755-0998.12958
citation: pmcid:PMC6469578
citation: pubmed:30362291
description: Individual-based model for simulating the evolution of tree populations in spatially and temporally heterogeneous landscapes.
feature list: operation_0282
feature list: operation 2426
feature list: operation 3196
is accessible for free: true
license: GPL-3.0
software help: metapop-user-documentation.pdf
primary contact: Antoine Kremer
primary contact: Armel Thöni
primary contact: Jean-Paul Soularue

Metascape
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0602
application sub category: topic 3172
citation: s41467-019-09234-6
citation: pmcid:PMC6447622
citation: pubmed:30944313
description: Portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists.
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: menu/faq
software help: menu/manual
software help: menu/manual meta
software help: menu/quickguide

MethBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3173
application sub category: topic 3295
citation: journal.pone.0081148
citation: pmcid:PMC3855694
citation: pubmed:24324667
description: A reference methylome database for different organisms that is created from public BS-seq datasets.
feature list: operation_0564
feature list: operation 3204
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: methbase-manual.pdf

MethylCal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0749
application sub category: topic 3295
application sub category: topic 3674
citation: gkz325
citation: pmcid:PMC6698668
citation: pubmed:31049595
description: Bayesian calibration of methylation levels | This package allows the calibration of methylation levels using MethylCal, a Bayesian calibration tool based on INLA (Rue et al., 2009). The package permits the visualisation of the calibration curve derived from standard controls with known methylation percentages for a selected assay. It also allows the correction of the methylation levels in case and control samples. If cases are provided, MethylCal performs a differential methylation test to detect hyper- and hypo-methylated samples. Besides MethylCal method, the package also includes the calibration and the correction provided by two alternative methods (Warnecke et al., 1997; Moskalev et al., 2011)
feature list: operation_0417
feature list: operation 3206
feature list: operation 3207
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Leonardo Bottolo
primary contact: Verena Zuber

MethylSeqDesign
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3295
application sub category: topic 3518
application sub category: topic 3674
citation: kxz016
citation: pmcid:PMC7846147
citation: pubmed:31107532
description: Framework for Methyl-Seq genome-wide power calculation and study design issues.
feature list: operation_0417
feature list: operation 3186
feature list: operation 3206
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: George Tseng

MethylToSNP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0632
application sub category: topic 2885
application sub category: topic 3295
application sub category: topic 3518
application sub category: topic 3674
citation: S13072-019-0321-6
citation: pmcid:PMC6923858
citation: pubmed:31861999
description: Identifying SNPs in Illumina DNA methylation array data. Detect SNP patterns in Methylation Array data. This is the developer version of Bioconductor package MethylToSNP. Install in R as:
feature list: operation_0308
feature list: operation_0484
feature list: operation 3186
feature list: operation 3196
feature list: operation 3661

MetumpX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 3172
application sub category: topic 3520
citation: BTZ765
citation: pubmed:31596440
description: A Metabolomics Support Package for Untargeted Mass Spectrometry. A Metabolomics Support Package for Untargeted Mass Spectrometery. MetumpX is a Ubuntu based software package that facilitate easy download and installation of about 89 tools related to standard Untargeted Metabolomics Mass Spectrometery pipeline. Installation • Authors • License • Revision History
feature list: operation 3627
feature list: operation 3767
feature list: operation 3860
license: GPL-3.0

MiCA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic 3382
application sub category: topic 3518
citation: J.COMPBIOMED.2019.103561
citation: pubmed:31785415
description: An extended tool for microarray gene expression analysis. Gene expression microarrays capture a complete image of all the transcriptional activity in a biological sample. Microarrays produce a large amount of data, which becomes a challenge when it comes to exploring and interpreting using modern computational and statistical tools. We propose the Microarray Analysis (MiCA) tool that outperforms other similar tools both in terms of ease of use and statistical features requiring minimal input to conduct an analysis. MiCA is an integrated, interactive, and streamlined desktop software for the analysis of microarray gene expression data. MiCA consists of a complete microarray analysis pipeline including but not limited to fetching data directly from GEO, normalization, interactive quality control, batch-effect correction, regression analysis, surrogate variable analysis and functional annotation methods such as GSVA using known existing R packages.
feature list: operation 2428
feature list: operation 2495
feature list: operation 3501
feature list: operation 3659

MiDRMpol
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic 3168
application sub category: topic 3301
citation: V11090806
citation: pmcid:PMC6784143
citation: pubmed:31480341
description: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors | A high-throughput multiplexed amplicon sequencing workflow to quantify drug resistance mutations (DRMs) against protease, reverse transcriptase and integrase inhibitors. MiDRMpol is computational as well as labor efficient bioinformatics pipeline to detect DRMs from HTS data.The method can be incorporated in large scale surveillance of HIV-1 DRMs
feature list: operation 3192
feature list: operation 3196

MiGMAP
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
  encoding format: format 2182
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic 2830
description: Mapper for full-length T- and B-cell repertoire sequencing.
feature list: operation 2403
feature list: operation 3198
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Mikhail Shugay

MiPepid
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0659
application sub category: topic 3306
application sub category: topic 3474
application sub category: topic 3512
citation: S12859-019-3033-9
citation: pmcid:PMC6842143
citation: pubmed:31703551
description: MicroPeptide identification tool using machine learning. MiPepid is a software specifically for predicting the coding capabilities of sORFs. Given a fasta file containing DNA fasta sequences, for each sequence, MiPepid will find all the sORFs (length <= 303 bp) present in all the 3 translation frames of the sequence, and for each sORF it will return the predicted class label (coding or noncoding) as well as the probability of being in that class. All the results will be written in an output .csv file
feature list: operation_0436
feature list: operation 3659
feature list: operation 3792

MiStImm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2830
application sub category: topic 3400
application sub category: topic 3524
citation: S12976-019-0105-5
citation: pmcid:PMC6498635
citation: pubmed:31046789
description: Agent-based simulation tool to study the self-nonself discrimination of the adaptive immune response.
feature list: operation_0478
feature list: operation 2426
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Windows
software help: README.txt
primary contact: 0000-0001-9541-246X

MiXCR
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
  encoding format: format 2182
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0160
application sub category: topic 2830
citation: nmeth.3364
description: Software for extraction of T- and B-cell receptor repertoires from any type of sequencing data.
feature list: operation_0292
feature list: operation_0310
feature list: operation 2403
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.html

MicroHibro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3301
citation: j.ijfoodmicro.2018.10.007
citation: pubmed:30368088
description: Software tool for predictive microbiology and microbial risk assessment in foods.
feature list: operation 2426
feature list: operation 3461
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

MicroPro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: S13059-019-1773-5
citation: pmcid:PMC6683435
citation: pubmed:31387630
description: Using metagenomic unmapped reads to provide insights into human microbiota and disease associations | A microbial profiling framework for metagenomic analysis | MicroPro is a software to perform profiling of both known and unknown microbial organisms for metagenomic dataset. A microbe is considered known/unknown if its whole genome is known/unknown according to the NCBI Reference Sequence Database. MicroPro has two pipelines: MicrobialPip and ViralPip. MicrobialPip considers all the microbial organisms including bacteria, archaea and viruses while ViralPip only extracts known and unknown viruses from the provided metagenomics dataset. More details of MicroPro are provided in the following paper:
feature list: operation_0362
feature list: operation 2495
feature list: operation 3730
license: GPL-3.0

MicroScope platform
type: SoftwareApplication
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1931
input: RefSeq accession
  type: FormalParameter
  additional type: data 1098
input: Sequence assembly
  type: FormalParameter
  additional type: data_0925
  encoding format: format 1929
input: Sequence assembly
  type: FormalParameter
  additional type: data_0925
  encoding format: format 1929
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1931
input: RefSeq accession
  type: FormalParameter
  additional type: data 1098
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1931
input: Sequence assembly
  type: FormalParameter
  additional type: data_0925
  encoding format: format 1929
output: Annotation track
  type: FormalParameter
  additional type: data 3002
  encoding format: format 1936
output: Sequence report
  type: FormalParameter
  additional type: data 2955
  encoding format: format 1929
  encoding format: format 1936
output: Annotation track
  type: FormalParameter
  additional type: data 3002
  encoding format: format 1936
output: Sequence composition plot
  type: FormalParameter
  additional type: data 2166
output: Annotation track
  type: FormalParameter
  additional type: data 3002
  encoding format: format 1936
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
additional type: Web application
additional type: Workbench
application sub category: topic_0085
application sub category: topic_0219
application sub category: topic_0621
application sub category: topic_0797
application sub category: topic 2259
application sub category: topic 3301
author: LABGeM - CEA/Genosocope - UMR8030
citation: bbx113
citation: bap021
citation: gkj406
citation: gks1194
citation: gkw1101
citation: gkz926
citation: pubmed:28968784
citation: pubmed:31647104
description: MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.
feature list: operation_0258
feature list: operation_0291
feature list: operation_0292
feature list: operation_0305
feature list: operation_0337
feature list: operation_0346
feature list: operation_0349
feature list: operation_0362
feature list: operation 2421
feature list: operation 2422
feature list: operation 2454
feature list: operation 2495
feature list: operation 2945
feature list: operation 3197
feature list: operation 3208
feature list: operation 3209
feature list: operation 3223
feature list: operation 3227
feature list: operation 3431
feature list: operation 3660
feature list: operation 3672
feature list: operation 3680
feature list: operation 3925
feature list: operation 3926
feature list: operation 3928
feature list: operation 3929
is accessible for free: true
provider: LABGeM - CEA/Genosocope - UMR8030
software help: stable
software help: microscopecharter.php
software help: services.php
primary contact: LABGeM - CEA/Genosocope - UMR8030

MicroWineBar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: https://doi.org/10.1101/742684
description: Analysing complex metagenomic data with MicroWineBar | MicroWineBar is a graphical tool for analysing metagenomic sequencing samples | MicroWineBar was designed for species abundance tables from shotgun metagenomics data but can also be used for other types of hierarchical data. The tab-delimited files contain absolute and/or relative abundances with taxonomic annotations (or other hierarchical data). As MicroWineBar is not tight to any specific program which generates species abundance tables, one needs to prepare the input:
feature list: operation_0362
feature list: operation 2939
feature list: operation 3891
license: MIT

Microbe Directory
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 3324
application sub category: topic 3697
citation: https://doi.org/10.1101/2019.12.20.860569
description: An Expanded Database of Ecological and Phenotypical Features of Microbes. Microbial communities are an incredibly fascinating and genetically diverse set of organisms that live with us, in us, and around us! Explore them all using the Microbe Directory, an inventory that profiles more than 7500 microbes!.
feature list: operation 2422
feature list: operation 3200

MicrobioLink
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic_0610
application sub category: topic 3063
application sub category: topic 3810
citation: https://doi.org/10.1101/837062
description: An integrated computational pipeline to infer functional effects of microbiome-host interactions. Abstract Microbiome-host interactions are important to nearly all living organisms, and play important roles in health and disease. Understanding these inter-kingdom cross-talks has a huge potential to advance diverse scientific domains such as the clinical and medical sciences, agriculture, and ecology. Detecting such interactions by experimental techniques remain challenging from a cost and feasibility perspective thus hampering large-scale analyses. Computational approaches not only make the inference of microbiome-host interactions viable but also scalable. Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins with host molecular networks.
feature list: operation 2492
feature list: operation 3439
feature list: operation 3461

MicrobiomeR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3174
application sub category: topic 3697
author: http://orcid.org/0000-0002-7687-0059
citation: joss.01299
description: MicrobiomeR is an R package for microbiome analysis that incorporates phyloseq, metacoder, taxa, and microbiome in order to standardize and simplify common microbiome workflows.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Windows
software help: microbiomer.vallenderlab.science
software version: 0.6.1
primary contact: http://orcid.org/0000-0001-8096-0180

Microdatasus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0611
application sub category: topic 3063
application sub category: topic 3473
citation: 0102-311X00032419
citation: pubmed:31531513
description: A package for downloading and preprocessing microdata from Brazilian Health Informatics Department (DATASUS)] | Download de dados do DataSUS e pré-processamento no R | O pacote para o R microdatasus apresenta funções para download dos arquivos de microdados do DataSUS (formato DBC), leitura dos arquivos através do pacote read.dbc e pré-processamento para utilização. Nesta última etapa, os rótulos e formato das variáveis são atribuídos e tratados | Plano Diretor de Tecnologia da Informação do Ministério da Saúde, biênio 2017-2018, foi publicada no Diário Oficial da União | Software de gestão hospitalar completo, desenvolvido em tecnologia web que substitui o sistema HOSPUB
feature list: operation 3644
license: GPL-3.0

Midcor
type: SoftwareApplication
input: Mass spectrum
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3835
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3835
output: Mass spectrum
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3835
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3172
application sub category: topic 3955
citation: 978-1-0716-0159-4 12
citation: s12859-017-1513-3
citation: pmcid:PMC5291980
citation: pubmed:28158972
citation: pubmed:31893378
description: R-program supporting a step of workflow of fluxomic analysis of artificial 13C labeling of metabolites. It designed to correct raw mass spectra (MS) of 13C-labeled metabolites of interest for natural isotopes occurrence. The raw mass spectra are supposed to be extracted from MS recording by Ramid.
feature list: operation 3860
license: Freeware
operating system: Linux
software help: ramidcor
software version: 0.0.1.0

MinION
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3293
application sub category: topic 3301
application sub category: topic 3305
application sub category: topic 3673
citation: S41598-019-52424-X
citation: pmcid:PMC6841976
citation: pubmed:31704961
description: Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology. Workflow and supporting files for Taylor et al: "Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology". Companion materials for the manuscript "Taylor et al: Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology". This repository contains the primary Nextflow workflow (minion_bacterial.nf) for bacterial nanopore assembly described in the manuscript and accessory scripts for reproducing the results therein. Workflows for the phylogenetic analysis can be run separately from the phylogenetics directory. The time series analysis can be reproduced using the following steps:.
feature list: operation_0310
feature list: operation 3192
feature list: operation 3644

Minerva
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 3174
application sub category: topic 3837
citation: gr.235499.118
citation: pmcid:PMC6314158
citation: pubmed:30523036
description: Alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics.
feature list: operation 3192
feature list: operation 3200
feature list: operation 3629
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: David C. Danko

MiniScrub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3474
application sub category: topic 3673
citation: S12859-019-3103-Z
citation: pmcid:PMC6833143
citation: pubmed:31694525
description: De novo Nanopore read quality improvement using deep learning. BACKGROUND:Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area. RESULTS:Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent "scrubbing" (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments
feature list: operation_0524
feature list: operation_0525
feature list: operation 3185
feature list: operation 3219
feature list: operation 3644

Miso
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic 3172
citation: btz092
citation: pubmed:30726876
description: R Package for Multiple Isotope Labeling Assisted Metabolomics Data Analysis.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Miso
software version: 0.2.1
primary contact: Yonghui Dong

MitoIMP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0654
application sub category: topic 3168
citation: https://doi.org/10.1177/1177932219873884
citation: pmcid:PMC6732850
citation: pubmed:31523131
description: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome | Ishiya, K., Mizuno, F., Wang, L., & Ueda, S. (2019). MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome. Bioinformatics and biology insights
feature list: operation 3196
feature list: operation 3211
feature list: operation 3557
license: MIT

MitoImpute
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3168
application sub category: topic 3384
application sub category: topic 3518
citation: https://doi.org/10.1101/649293
description: Snakemake pipeline for imputation of mitochondrial genetic variants using Impute2 Chromosome X protocol.
feature list: operation 3196
feature list: operation 3557
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Shea J. Andrews

MixMPLN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3697
application sub category: topic 3855
citation: BTZ370
citation: pmcid:PMC6612855
citation: pubmed:31510709
description: Learning a mixture of microbial networks using minorization-maximization | "MixMPLN" is a package written in R, which has two features. First feature is generating a proper synthetic sample-taxa count matrix. Second feature is receiving a sample-taxa count matrix and extracting k(number of components) different interaction networks between taxa | Following packages must be installed and loaded in R environment before using "MixMPLN":
feature list: operation 2937
feature list: operation 3192

Mizutama
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3300
application sub category: topic 3382
application sub category: topic 3500
citation: https://doi.org/10.1086/702666
citation: pubmed:30730249
description: Image-processing software developed for counting cells in photographs of blood smears.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Gregorio Moreno-Rueda

MoBPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3297
citation: https://doi.org/10.1101/829333
description: Modular Breeding Program Simulator. This repository contains our R-package MoBPS and the associated packages (miraculix/RandomFieldsUtils/MoBPSmaps). A manuscript for the package is finally available in preprint (https://www.biorxiv.org/content/10.1101/829333v1)
feature list: operation 3196
feature list: operation 3891
license: GPL-3.0

MoChA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic_0654
application sub category: topic 3399
application sub category: topic 3518
citation: pmcid:PMC6846495
description: CLONAL HEMATOPOIESIS IN A CENTENARIAN COHORT. MOsaic CHromosomal Alterations (MoChA) caller. A bcftools extension to call mosaic chromosomal alterations starting from phased VCF files with either B Allele Frequency (BAF) and Log R Ratio (LRR) or allelic depth (AD). If you use this tool in your publication, please cite the following paper and preprint:. This command will create a list of variants falling within segmental duplications with low divergence (<2%), high levels of missingness (>2%), variants with excess heterozygosity (p<1e-6), and variants that correlate with sex in an unexpected way (p<1e-6).
feature list: operation 3196
feature list: operation 3227
feature list: operation 3454

MoMI-G
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0622
application sub category: topic 3168
application sub category: topic 3175
application sub category: topic 3512
citation: S12859-019-3145-2
citation: pmcid:PMC6833150
citation: pubmed:31690272
description: Modular multi-scale integrated genome graph browser. Long-read sequencing allows for more sensitive and accurate discovery of SVs, which requires to filter and validate thousands of candidates. However, no existing genome browser meets the demand for cancer genomics. Because most visualization tools show an only range of a linear sequence, making them unsuitable for large (over megabase) or nested SVs. Also, no existing genome browsers allow users to simultaneously inspect the read alignments that span the reference allele and an alternative allele caused by a heterozygous SV. Here we present MoMI-G, a graph genome browser to visualize SVs on the variation graph, that provides a graph-based view that displays a genome with branches and alignments on them. Users can filter, visualize with genomic annotations, and inspect SVs with read alignments. A genome graph browser for visualization of structural variants (SVs) as a variation graph:
feature list: operation 3182
feature list: operation 3198
feature list: operation 3208
feature list: operation 3227
license: MIT

MoRF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0082
application sub category: topic 3474
application sub category: topic 3538
citation: BTZ691
citation: pubmed:31504193
description: Identifying Molecular Recognition Features in Intrinsically Disordered Regions of Proteins by Transfer Learning | AVAILABILITY HTML server, please click here. RESTful web server, please click here. (Updated Apr. 10, 2018) Downloadable software, please click here. OVERVIEW A new computational approach for a fast and accurate prediction of MoRFs in protein sequences. MoRFchibi SYSTEM (Malhis et al 2016) includes three different predictors: MoRFCHiBi is most appropriate as a component predictor in other applications. […] | The University of British Columbia
feature list: operation_0253
feature list: operation_0303
feature list: operation 3904

MoRFMPM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic_0749
application sub category: topic 2269
citation: S12859-019-3111-Z
citation: pmcid:PMC6819637
citation: pubmed:31660849
description: Computational prediction of MoRFs based on protein sequences and minimax probability machine. BACKGROUND:Molecular recognition features (MoRFs) are one important type of disordered segments that can promote specific protein-protein interactions. They are located within longer intrinsically disordered regions (IDRs), and undergo disorder-to-order transitions upon binding to their interaction partners. The functional importance of MoRFs and the limitation of experimental identification make it necessary to predict MoRFs accurately with computational methods. RESULTS:In this study, a new sequence-based method, named as MoRFMPM, is proposed for predicting MoRFs. MoRFMPM uses minimax probability machine (MPM) to predict MoRFs based on 16 features and 3 different windows, which neither relying on other predictors nor calculating the properties of the surrounding regions of MoRFs separately.
feature list: operation_0250
feature list: operation_0303
feature list: operation 3904

MobCal-MPI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0153
application sub category: topic 3520
citation: c8an02150c
citation: pubmed:30649115
description: Programfor calculation of ion or molecule collision cross sections on parallelized computing architectures.
feature list: operation_0386
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: MobCal-MPI
primary contact: C. Ieritano
primary contact: W. S. Hopkins

ModCell2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3407
citation: j.ymben.2018.09.003
citation: pubmed:30201314
description: Strain design framework for modular cell engineering.
feature list: operation 3660
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest
primary contact: TrinhLab - University of Tennessee Knoxville

ModEx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0218
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3169
citation: J.JBI.2019.103353
citation: pubmed:31857203
description: A text mining system for extracting mode of regulation of transcription factor-gene regulatory interaction. Deciphering the network of TF-target interactions with information on mode of regulation (activation vs. repression) is an important step toward understanding the regulatory pathways that underlie complex traits. There are many experimental, computational, and manually curated databases of TF-gene interactions. In particular, high-throughput ChIP-seq datasets provide a large-scale map or transcriptional regulatory interactions. ModEx can be installed using the GitHub repository. All of the dependencies will be installed via setup.py script. Saman Farahmand, Todd Riley, Kourosh Zarringhalam, "ModEx: A text mining system for extracting mode of regulation of Transcription Factor-gene regulatory interaction", BioRxiv, 2019
feature list: operation_0306
feature list: operation 1781
feature list: operation 3439
license: MIT

ModMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: A data warehouse for the modENCODE project
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 33 28JUL2014

ModelExplorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic 3407
citation: s12859-019-2615-x
citation: pmcid:PMC6348647
citation: pubmed:30691403
description: Software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions.
feature list: operation 3660
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ModelExplorer2.0 Linux.zip
software help: ModelExplorer2.0 win64.zip
software version: 2.0
primary contact: Eivind Almaas

ModelTest-NG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 3293
application sub category: topic 3316
citation: msz189
citation: pmcid:PMC6984357
citation: pubmed:31432070
description: A new and scalable tool for the selection of DNA and protein evolutionary models | ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces
feature list: operation 3798
license: GPL-3.0

ModelX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic_0659
application sub category: topic 2275
application sub category: topic 3512
citation: PNAS.1910999116
citation: pmcid:PMC6900601
citation: pubmed:31732673
description: Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX. ModelX: A toolsuite for molecular modeling. ModelX is a toolsuite for biomolecular modeling inspired on the assumption that Molecular Biology conformational landscape is huge but limited, and also on the fact that interactions between biological entities can be decomposed into small structural motifs that are recycled and reused by nature while shaping new relationships.
feature list: operation 3216
feature list: operation 3899
feature list: operation 3900
feature list: operation 3901
feature list: operation 3902

MolArt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0601
citation: bty489
citation: pmcid:PMC6247942
citation: pubmed:29931246
description: MolArt (MOLeculAR structure annoTator) - molecular structure annotation and visualization tool.
feature list: operation_0564
feature list: operation_0570
is accessible for free: true
license: Apache-2.0
software help: README.md
primary contact: https://orcid.org/0000-0003-4679-0557

MolMeDB
type: SoftwareApplication
input: Compound name
  type: FormalParameter
  additional type: data_0990
  encoding format: format 1964
output: Experiment report
  type: FormalParameter
  additional type: data 2531
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0202
application sub category: topic 3068
application sub category: topic 3292
application sub category: topic 3332
author: http://orcid.org/0000-0003-3393-3010
author: Jakub Juračka
citation: https://doi.org/10.1101/472167
contributor: http://orcid.org/0000-0001-9472-2589
contributor: http://orcid.org/0000-0001-9556-2978
contributor: Michaela Melíková
description: MolMeDB is an open chemistry database about interactions of molecules with membranes.
feature list: operation 2422
feature list: operation 3431
funder: Czech Grant Agency
is accessible for free: true
license: CC-BY-4.0
software help: contact
software help: documentation
primary contact: http://orcid.org/0000-0001-9472-2589

Molecular clock
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0199
application sub category: topic 2814
citation: SYZ022
citation: pubmed:31111152
description: Computation of clock violations.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Ugo Bastolla

Monarch Initiative
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3390
citation: gkz997
citation: pmcid:PMC7056945
citation: pubmed:31701156
description: An integrative data and analytic platform connecting phenotypes to genotypes across species. Combine genotype and phenotype data across species for patient variant prioritization, functional annotation and pathogenicity determination. Securely share & discuss patients with colleagues all around the world.
feature list: operation_0306
feature list: operation 3196
feature list: operation 3226
feature list: operation 3778

MonkeyLogic
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3077
application sub category: topic 3300
citation: j.jneumeth.2019.05.002
citation: pmcid:PMC6743332
citation: pubmed:31071345
description: Software tool for behavioral control and data acquisition.
is accessible for free: true
license: Unlicense
operating system: Windows
software help: docs.html

MaGIC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3169
application sub category: topic 3179
application sub category: topic 3295
citation: s12859-019-2679-7
citation: pmcid:PMC6394031
citation: pubmed:30819107
description: Monoallelic Gene Inference from Chromatin (MaGIC) - tool to classify genes into monoallelically expressed (MAE) and biallelically expressed (BAE) using chromatin mark enrichment data.
feature list: operation 3227
feature list: operation 3501
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: documentation.md
primary contact: Alexander Gimelbrant
primary contact: Henry Ward
primary contact: Sachit Saksena
primary contact: Svetlana Vinogradova
primary contact: Sébastien Vigneau

Monoallelic gene inference from chromatin (MaGIC)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3169
application sub category: topic 3179
application sub category: topic 3295
citation: s12859-019-2679-7
citation: pmcid:PMC6394031
citation: pubmed:30819107
description: Machine learning tool set and web application for monoallelic gene inference from chromatin. Classifies genes into monoallelically expressed (MAE) and biallelically expressed (BAE) using chromatin mark enrichment data.
feature list: operation 3227
feature list: operation 3501
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
primary contact: Alexander Gimelbrant
primary contact: Henry Ward
primary contact: Sachit Saksena
primary contact: Svetlana Vinogradova
primary contact: Sébastien Vigneau

MoonDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0623
description: MoonDB is a database containing predicted Extreme Multifunctional (EMF) proteins (i.e. proteins with several unrelated functions), as well as a set of manually curated moonlighting proteins. Moonlighting proteins are a subclass of multifunctional proteins.

MorphoCatcher
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0632
application sub category: topic 3168
citation: PEERJ.6801
citation: pmcid:PMC6487805
citation: pubmed:31086739
description: Multiple-alignment based web tool for target selection and designing taxon-specific primers in the loop-mediated isothermal amplification method.
feature list: operation_0308
feature list: operation 3192
feature list: operation 3237
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Manual.pdf
software help: Tutorials.zip
primary contact: Fedor V. Shirshikov

MotifAnalyzer-PDZ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic_0160
application sub category: topic_0736
citation: PRO.3741
citation: pmcid:PMC6863708
citation: pubmed:31599029
description: A computational program to investigate the evolution of PDZ-binding target specificity. PDZ domains bind the extreme C-terminus of target proteins and are critical components of signaling and trafficking pathways. MotifAnalyzer-PDZ identifies enrichment trends for specific amino acids in a PDZ-binding motif-satisfying sequence across multiple organisms
feature list: operation_0239
feature list: operation_0303
feature list: operation 2492

MouseBytes
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic_0769
application sub category: topic 3304
application sub category: topic 3489
citation: ELIFE.49630
citation: pmcid:PMC6934379
citation: pubmed:31825307
description: Open-access high-throughput pipeline and database for rodent touchscreen-based cognitive assessment. Mousebytes-An-open-access-high-throughput-pipeline-and-database-for-rodent-touchscreen-based-data. This code is associated with the paper from Beraldo et al., "MouseBytes, an open-access high-throughput pipeline and database for rodent touchscreen-based cognitive assessment". eLife, 2019. http://dx.doi.org/10.7554/eLife.49630. Quality control (QC) procedure in MouseBytes checks the content of xml files against the potential errors and flag the files that do not meet the criteria (refer to "QC Documents" folder). Such xml files belong to a cognitive task experimented using Bussey-Saksida Mouse Touchscreen System and exported via ABET II software. Note that each xml file must contain the machine-generated (ABET II) features like "Analysis Name", "Schedule Name", "Max_Number_Trials", and "Max_Schedule_Time"
feature list: operation_0335
feature list: operation 3196
feature list: operation 3431
license: GPL-3.0

Mouse Phenome Database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0654
application sub category: topic 3298
application sub category: topic 3300
application sub category: topic 3500
citation: gkz1032
citation: pmcid:PMC7145612
citation: pubmed:31696236
description: A data repository and analysis suite for curated primary mouse phenotype data. Available genotype resources and tools. RESTful API for getting data and metadata. Already have an account? Sign In. ...an integrated resource to explore physiology
feature list: operation 2421
feature list: operation 2422
feature list: operation 3196
feature list: operation 3557
software help: api

MrNV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0602
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: S12864-019-6102-6
citation: pmcid:PMC6805343
citation: pubmed:31640560
description: Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection. Data analysis pipeline used for the assembly and differential abundance analysis of M. rosenbergii transcriptome in response to MrNV infection. Transcriptomic analysis (RNAseq) of Macrobrachium rosenbergii post-larvae in response to Macrobrachium rosenbergii nodavirus (MrNV) infection. Phongthana Pasookhush, Charles Hindmarch, Siwaporn Longyant, Paisarn Sithigorngul, William G. Bendena, Parin Chaivisuthangkura. Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) postlarvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation. BMC Genomics volume 20, Article number: 762 (2019), DOI: 10.1186/s12864-019-6102-6 Article URL
feature list: operation_0524
feature list: operation 3192
feature list: operation 3258
feature list: operation 3800

MsPAC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic 3168
citation: btz618
citation: pmcid:PMC7523683
citation: pubmed:31397844
description: Tool for haplotype-phased structural variant detection.
feature list: operation_0525
feature list: operation 3227
feature list: operation 3454
is accessible for free: true
license: Unlicense
operating system: Linux
software help: README.md
primary contact: Oscar L. Rodriguez

MtBNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3474
application sub category: topic 3517
citation: BTZ767
citation: pubmed:31693090
description: Quantifying Functional Impact of Noncoding Variants with Multi-task Bayesian Neural Network. The python script for MtBNN. The help information can be obtain by
feature list: operation_0484
feature list: operation 3196
feature list: operation 3226
license: MIT

MuLan-Methyl
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Multiple transformer-based language models for accurate DNA methylation prediction
software version: 1.02

MuLiMs-MCoMPAs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0154
application sub category: topic_0736
application sub category: topic 3314
citation: ACS.JCIM.9B00629
citation: pubmed:31663741
description: A Novel Multiplatform Framework to Compute Tensor Algebra-Based Three-Dimensional Protein Descriptors. MuLiMs-MCoMPAs software is for the calculation of 3D bio macromolecular (protein and peptide) descriptors based on the two-linear and three-linear algebraic. …methods and tools for Chem-Bio-Med-Informatic Studies. MuLiMs-MCoMPAs software is for the calculation of 3D bio macromolecular (protein and peptide) descriptors based on the two-linear and three-linear algebraic forms
feature list: operation_0303
feature list: operation 3436
feature list: operation 3891

MuPIPR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic_0199
application sub category: topic 3474
citation: https://doi.org/10.1101/2019.12.15.876953
description: Mutation effect estimation on protein-protein interactions using deep contextualized representation learning. This is the repository for "Mutation effect estimation on protein-protein interactions using deep contextualized representation learning" (MuPIPR). This repository contains the source code and links to some datasets used in our paper. (to be updated)
feature list: operation_0272
feature list: operation_0331
feature list: operation 2492

MuSiC2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0199
application sub category: topic_0622
application sub category: topic 2269
application sub category: topic 2640
citation: gr.134635.111
citation: pmcid:PMC3409272
citation: pubmed:22759861
description: MuSiC2 ( Mutational Significance in Cancer) is a comprehensive mutational analysis pipeline that uses standardized sequence-based inputs along with multiple types of clinical data to establish correlations among mutation sites, affected genes and pathways, and to ultimately separate the commonly abundant passenger mutations from the truly significant events.
feature list: operation_0362
feature list: operation 2454
feature list: operation 3197
feature list: operation 3225
feature list: operation 3504
is accessible for free: true
license: MIT
operating system: Linux
software help: documentation.html
software help: README.md
software version: 0.2
primary contact: https://orcid.org/0000-0003-1517-2975

Multi-netclust
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0602
citation: btv479
citation: pmcid:PMC4576697
citation: pubmed:26330601
description: Tool for finding connected clusters in multi-parametric networks.
feature list: operation 3436
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Jack A.M. Leunissen

Multi-omics Visualization Platform
type: SoftwareApplication
input: Peptide identifier
  type: FormalParameter
  additional type: data_0988
  encoding format: format 3681
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3922
description: A plug-in to the Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using a multi-omic proteogenomic approach.
feature list: operation_0337
is accessible for free: true
license: MIT
software help: tutorial.html

MultiGuideScan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0099
application sub category: topic_0654
application sub category: topic 3168
citation: btz616
description: Multi-processing tool for designing CRISPR guide RNA libraries.
feature list: operation 3096
feature list: operation 3216
is accessible for free: true
license: Other
operating system: Linux
software help: README.md
primary contact: Jianxin Wang

MultiWaver
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3056
application sub category: topic 3299
citation: s41431-018-0259-3
citation: pmcid:PMC6303267
citation: pubmed:30206356
description: Models discrete and continuous gene flow to reconstruct complex population admixtures.
feature list: operation_0487
feature list: operation 3196
feature list: operation 3745
is accessible for free: true
operating system: Linux
operating system: Mac
software version: 2.0
primary contact: Shuhua Xu

MultiXcan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3337
application sub category: topic 3517
citation: journal.pgen.1007889
citation: pmcid:PMC6358100
citation: pubmed:30668570
description: Set of tools to perform integrative gene mapping studies.
feature list: operation 3196
feature list: operation 3232
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

Multilayer Extraction
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
citation: pmcid:PMC6927681
citation: pubmed:31871433
description: Community Extraction in Multilayer Networks with Heterogeneous Community Structure. An R package to identify strongly connected vertex-layer communities in multilayer networks. An R package that implements the multilayer extraction algorithm to identify densely connected vertex-layer sets in multilayer networks. multilayer.extraction(): identify densely connected vertex-layer communities within multilayer networks. This is a significance based approach that seeks to optimize a score derived from the strength of connection within multilayer communities. See the above reference for more details.
feature list: operation_0337
feature list: operation 3432

MultimodalPrognosis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3474
citation: BTZ342
citation: pmcid:PMC6612862
citation: pubmed:31510656
description: Deep learning with multimodal representation for pancancer prognosis prediction | Our model estimates the time-til-death for patients across 20 different cancer types using the vast amount of multimodal data that is available for cancer patients | git clone https://github.com/gevaertlab/MultimodalPrognosis | For more details, see our paper
feature list: operation 3891

Multiple Myeloma survival prediction
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: This is the dockerized environment for the winning algorithm in the 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3.
license: GPL-3.0
operating system: Linux

Muscle2View
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0769
application sub category: topic 3382
citation: JAPPLPHYSIOL.00257.2019
citation: pubmed:31697593
description: CellProfiler pipeline for detection of the capillary-to-muscle fiber interface and high-content quantification of fiber type-specific histology. Because manual immunohistochemical analysis of features such as skeletal muscle fiber typing, capillaries, myonuclei, and fiber size-related parameters is time consuming and prone to user subjectivity, automatic computational methods could allow for faster and more objective evaluation. Here, we developed Muscle2View, a free CellProfiler-based pipeline that integrates all key fiber-morphological variables, including the novel quantification of the capillary-to-fiber interface, in one single tool. Provided that the images are of sufficient quality and the settings are configured for the specific study, the pipeline allows for automatic and unsupervised analysis of fiber borders, myonuclei, capillaries, and morphometric parameters in a fiber type-specific manner from large batches of images in <10 min tissue sample.
feature list: operation 3443
feature list: operation 3799

Muscle Gene Sets
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Ontology
application sub category: topic_0634
application sub category: topic 3308
application sub category: topic 3517
citation: S13395-019-0196-Z
citation: pmcid:PMC6498474
citation: pubmed:31053169
description: Versatile methodological aid to functional genomics in the neuromuscular field.
feature list: operation_0571
feature list: operation 2436
feature list: operation 3223
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0003-2239-9094

MutEx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3170
citation: bbz084
citation: pmcid:PMC7373173
citation: pubmed:31588509
description: A multifaceted gateway for exploring integrative pan-cancer genomic data. Somatic mutation and gene expression dysregulation are considered two major tumorigenesis factors. While independent investigations of either factor pervade, studies of associations between somatic mutations and gene expression changes have been sporadic and nonsystematic. Utilizing genomic data collected from 11 315 subjects of 33 distinct cancer types, we constructed MutEx, a pan-cancer integrative genomic database. This database records the relationships among gene expression, somatic mutation and survival data for cancer patients. MutEx can be used to swiftly explore the relationship between these genomic clinic features within and across cancer types and, more importantly, search for corroborating evidence for hypothesis inception.
feature list: operation 2421
feature list: operation 2495
feature list: operation 3223

MutSig2CV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web service
application sub category: topic_0199
application sub category: topic_0622
application sub category: topic 2269
application sub category: topic 2640
citation: nature12213
citation: nature12912
citation: pmcid:PMC3919509
citation: pmcid:PMC4048962
citation: pubmed:23770567
citation: pubmed:24390350
description: MutSig stands for "Mutation Significance". MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.
feature list: operation 2454
feature list: operation 3197
feature list: operation 3225
feature list: operation 3504
is accessible for free: true
operating system: Linux
software help: mutsig
software version: 2.0
primary contact: Michael S. Lawrence

MutSpot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3173
citation: https://doi.org/10.1101/740944
description: Detection of non-coding mutation hotspots in cancer genomes | Non-coding MUTation hotSPOT dectection in cancer genomes | The MutSpot R package systematically and unbiasedly scans cancer whole genomes to detect mutation hotspots. MutSpot first builds a background mutation model that corrects for covariates of mutation probability, such as local nucleotide context, replication timing and epigenomic features. Then MutSpot evaluates the mutation recurrence of focal DNA regions using a Poisson binomial model to account for varying mutation rates across different tumors. Mutation hotspots identified have significantly higher mutation recurrence compared to the background genomic mutation rate, suggesting positive selection in cancer and involvement in tumorigenesis
feature list: operation 3202
feature list: operation 3798

MutaFrame
type: SoftwareApplication
input: UniProt accession
  type: FormalParameter
  additional type: data 3021
output: Protein features
  type: FormalParameter
  additional type: data 1277
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic 3510
citation: gkx390
citation: pmcid:PMC5570203
citation: pubmed:28498993
description: Variant effect prediction with interpretation at the protein structure level
feature list: operation_0331
feature list: operation_0570
is accessible for free: true

MutaNET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic_0749
citation: btx687
citation: pmcid:PMC6192214
citation: pubmed:29087464
description: Tool for automated analysis of genomic mutations in gene regulatory networks.
feature list: operation_0277
feature list: operation 1781
feature list: operation 3439
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: user guide.html
primary contact: Volkhard Helms

MutateX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0130
application sub category: topic_0199
application sub category: topic_0601
application sub category: topic_0821
application sub category: topic 3297
citation: https://doi.org/10.1101/824938
description: an automated pipeline for in-silico saturation mutagenesis of protein structures and structural ensembles. scripts and facilities for in-silico mutagenesis with FoldX. Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark. MutateX: an automated pipeline for in-silico saturation mutagenesis of protein structures and structural ensembles Matteo Tiberti, Thilde Terkelsen, Tycho Canter Cremers, Miriam Di Marco, Isabelle da Piedade, Emiliano Maiani, Elena Papaleo, submitted to biorxiv
feature list: operation_0307
feature list: operation_0331
feature list: operation_0417
license: GPL-3.0

Mutplot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0736
application sub category: topic 3068
citation: JOURNAL.PONE.0215838
citation: pmcid:PMC6519802
citation: pubmed:31091262
description: Tool for plotting complex mutation data with flexibility.
feature list: operation_0337
feature list: operation 3431
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0002-6123-8034

MySeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0208
application sub category: topic_0605
application sub category: topic_0625
application sub category: topic 3673
application sub category: topic 3676
citation: S12920-019-0615-3
citation: pmcid:PMC6882182
citation: pubmed:31775760
description: Privacy-protecting browser-based personal Genome analysis for genomics education and exploration. MySeq is a web-application for privacy-protecting interactive analysis of personal genomes (distributed as compressed-and-indexed VCF files) inspired by GENOtation (previously the Interpretome) and DNA.LAND Compass. MySeq is intended for use as a genomics educational platform. Analyzing the PTC Tasting Phenotype with MySeq. This page is an example analysis of the "bitter tasting" trait using the MySeq application in an embedded context. Here MySeq is used to both query a whole genome VCF for NA12878 (from Genome in a Bottle) by genomic coordinates and predict the bitter tasting phenotype directly. All of the queries demonstrated here are performed "live" in the browser, that is these are not pre-generated results. Try MySeq as a "standalone" application. MySeq is a single-page web application for privacy-protecting personal genome analysis
feature list: operation_0224
feature list: operation 1812
feature list: operation 3196
feature list: operation 3227
feature list: operation 3283

MyelinJ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3168
application sub category: topic 3304
application sub category: topic 3382
citation: btz403
citation: pmcid:PMC6821319
citation: pubmed:31095292
description: ImageJ macro for high throughput analysis of myelinating cultures.
feature list: operation 3435
feature list: operation 3450
is accessible for free: true
license: Unlicense
operating system: Mac
operating system: Windows
software help: README.md
software help: https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/PAP/10.1093_bioinformatics_btz403/3/btz403_supplementary_data.zip
primary contact: Susan Barnett

Mykrobe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic_0632
application sub category: topic 3174
application sub category: topic 3673
citation: WELLCOMEOPENRES.15603.1
citation: pmcid:PMC7004237
citation: pubmed:32055708
description: Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe. Antibiotic resistance prediction in minutes. Table of Contents generated with DocToc. AMR prediction (Mykrobe predictor). Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed
feature list: operation 3192
feature list: operation 3196
feature list: operation 3227
feature list: operation 3482
license: MIT

Myo-REG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0621
application sub category: topic 2229
application sub category: topic 3375
application sub category: topic 3489
citation: FPHYS.2019.01216
citation: pmcid:PMC6776608
citation: pubmed:31611808
description: A Portal for Signaling Interactions in Muscle Regeneration. myogenesis and regeneration portal. Myo-REG offers easy access to signaling information in the context of muscle regeneration. Myogenesis & REGeneration Portal. Myo-REG offers easy access to signaling information in the context of muscle regeneration. The information is organized in two layers: the first concerns cell-cell interactions, while the second layer describes the most relevant signaling pathways underlying the crosstalk between the cell types participating in muscle regeneration. A user-friendly interface allows users to explore, via an interactive model, cell and pathway crosstalk
feature list: operation_0224
feature list: operation 3096
feature list: operation 3562

N-GlycositeAtlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3510
citation: S12014-019-9254-0
citation: pmcid:PMC6731604
citation: pubmed:31516400
description: A database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping | Not a member? Reigist in www.biomarkercenter.org/nglycositeatlas | Database UniProtKB AC/ID Gene Protein Site Peptide Motif Source Year Reference
feature list: operation_0417
feature list: operation 2929
feature list: operation 3646

N1PAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 3170
application sub category: topic 3320
citation: FGENE.2019.00414
citation: pmcid:PMC6521780
citation: pubmed:31143202
description: Single-Subject Method to Detect Pathways Enriched With Alternatively Spliced Genes.
feature list: operation_0533
feature list: operation 3501
feature list: operation 3800
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Alfred Grant Schissler
primary contact: Yves A. Lussier

NACHO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0092
application sub category: topic_0632
application sub category: topic_0659
citation: btz647
citation: pmcid:PMC9883715
citation: pubmed:31504159
description: An R package for quality control of NanoString nCounter data | NACHO: NAnostring quality Control dasHbOard | NACHO does this by visualising quality control metrics, expression of control genes, principal components and sample specific size factors in an interactive web application
feature list: operation_0571
feature list: operation 2939
feature list: operation 3218
license: LGPL-3.0

NAGbinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic 3474
application sub category: topic 3534
citation: pro.3761
citation: pmcid:PMC6933864
citation: pubmed:31654438
description: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence. This is for predicting NAGbinding sites in a protein. A web server for predicting N-Acetylglucosamine (NAG) interacting residues in a protein. Home page of NAGbinder, which is a web based tool developed for predicting of NAG binding residues in a protein. NAGbinder is a Python-based tool for predicting NAG interacting residues in an uncharacterized protein chain. Prediction of NAG interacting residues. Reference: Patiyal et. al. (2019) NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence
feature list: operation_0272
feature list: operation_0321
feature list: operation 2575

NAMS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic_0780
citation: 978-1-4939-9045-0 15
citation: pubmed:30945190
description: Noncoding Assessment of long RNAs in Magnoliophyta Species.
feature list: operation 2495
is accessible for free: true
license: CC-BY-4.0
operating system: Linux

NBDC RDF Portal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic 3068
application sub category: topic 3071
citation: bay123
citation: pmcid:PMC6301334
citation: pubmed:30576482
description: Comprehensive repository for semantic data in life sciences.
feature list: operation 2422
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

NBGLM-LBC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: S12859-019-3017-9
citation: pmcid:PMC6693229
citation: pubmed:31409293
description: Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods | Library bias correction for multiplex RNAseq | Library bias correction for multiplex RNAseq. GitHub Gist: instantly share code, notes, and snippets | Instantly share code, notes, and snippets |
feature list: operation 3200
feature list: operation 3258
feature list: operation 3766

NCATS BioPlanet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic 2840
application sub category: topic 3369
citation: FPHAR.2019.00445
citation: pmcid:PMC6524730
citation: pubmed:31133849
description: Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics.
feature list: operation_0277
feature list: operation_0533
feature list: operation 3439
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial.html
primary contact: Ruili Huang

NCBI-protein
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: domain sequence-NES site

NCPHLDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3335
citation: C9MO00092E
citation: pubmed:31686064
description: A novel method for human lncRNA-disease association prediction based on network consistency projection. Copyright (C) 2019 Zecheng Huang(2111705162@mail2.gdut.edu.cn),Guobo Xie(xiegb@gdut.edu.cn). This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Type: Package Title: NCPHLDA:A Novel Method for Human LncRNA-Disease Association Prediction Based on Network Consistency Projection. To analyze these data on NCPHLDA to further infer potential associations between lncRNAs and diseases, you should input the appropriate code in the matlab Command Window:
feature list: operation 3435
feature list: operation 3439
license: GPL-2.0

NCutYX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0091
application sub category: topic_0203
application sub category: topic_0634
citation: btz842
citation: pmcid:PMC8597621
citation: pubmed:31730176
description: A package for clustering analysis of multilayer omics data. Clustering of Omics Data of Multiple Types with a Multilayer Network Representation. Omics data come in different forms: gene expression, methylation, copy number, protein measurements and more. 'NCutYX' allows clustering of variables, of samples, and both variables and samples (biclustering), while incorporating the dependencies across multiple types of Omics data. (SJ Teran Hidalgo et al (2017), <doi:10.1186/s12864-017-3990-1>)
feature list: operation 2495
feature list: operation 3432
feature list: operation 3435
license: GPL-3.0

NDD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3474
citation: S41598-019-50121-3
citation: pmcid:PMC6754439
citation: pubmed:31541145
description: Drug-Drug Interaction Predicting by Neural Network Using Integrated Similarity | Link of paper: https://www.nature.com/articles/s41598-019-50121-3 A Novel Method For Predicting Drug-Drug Interaction By Neural Network Due to the great importance of this issue in the economy, industry, and health, proposing appropriate computational methods for predicting unknown DDI with high precision is challenging. We propose a novel machine learning method for predicting unknown DDIs called "NDD", using a two-layer fully connected neural network. NDD uses various characteristics of drugs to have comprehensive information. Multiple drug similarities are calculated. NDD integrat various drug similarities with a non-linear similarity fusion method called "SNF" to achieve high-level features. Dependency: python version 3.5.3 deep learning lib keras: https://github.com/fchollet/keras/ machine learning lib scikit-learn: https://github.com/scikit-learn/scikit-learn Contact: nasim.rohani74@gmail.com
feature list: operation 3439
feature list: operation 3891
license: Apache-2.0

NERDSS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0153
application sub category: topic_0196
application sub category: topic_0602
application sub category: topic_0821
application sub category: topic 3512
citation: https://doi.org/10.1101/853614
description: A non-equilibrium simulator for multibody self-assembly at the cellular scale. NonEquilibrium Reaction-Diffusion Self-assembly Simulator. Additional documentation through doxygen can be found within docs/ by opening index.html
feature list: operation_0310
feature list: operation 2476
feature list: operation 3893
license: GPL-3.0

NET-EXPO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3305
application sub category: topic 3315
citation: 978-3-030-23525-3 1
citation: pmcid:PMC6738962
citation: pubmed:31511852
description: A Gephi Plugin Towards Social Network Analysis of Network Exposure for Unipartite and Bipartite Graphs | Gephi plugin for network exposure models | NET-EXPO is a Gelphi plugin that computes various types of network exposure metrics for the purpose of visualization exposure within a network for analysis. Currently network exposure model (Marsden, et al. 1993, Burt, 1987, Valente, 1996, 2005), affiliation exposure model (Fujimoto, et al., 2011, 2012), and limited support for decomposition exposure model (Fujimoto, 2012, Fujimoto, et al., 2013) are supported
feature list: operation 3766
feature list: operation 3891
license: Apache-2.0

NETGE-PLUS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0621
application sub category: topic_0625
author: Samuele Bovo
citation: https://doi.org/10.1101/750661
description: Standard and network-based gene enrichment analysis in human and model organisms | NETGE-PLUS is a web-server for standard and network-based functional interpretation of gene sets of human and model organisms | NETGE-PLUS is optimized to be used on a Google Chrome browser | NETGE-PLUS is a web-server for standard and network-based functional interpretation of gene sets of human and model organisms, including S. scrofa, S. cerevisiae, E. coli and A. thaliana
feature list: operation 2436
feature list: operation 3083
feature list: operation 3196
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-0274-5669
primary contact: ELIXIR-ITA-BOLOGNA
primary contact: Samuele Bovo

NETPAGE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic_0634
citation: https://doi.org/10.1101/781203
description: Network propagation of rare mutations in Alzheimer’s disease reveals tissue-specific hub genes and communities | Source code for network propagation | NETPAGE (NETwork Propagation-based Assessment of Genetic Events) is a novel computational framework for gene-based association testing of rare variants that integrates prior knowledge about tissue-specific gene interaction networks (Scelsi et al., in preparation)
feature list: operation 2436
feature list: operation 3196
feature list: operation 3435
license: GPL-3.0

NExUS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 2269
application sub category: topic 2640
citation: btz636
citation: pmcid:PMC8215919
citation: pubmed:31504175
description: Bayesian simultaneous network estimation across unequal sample sizes | --> 'Data_generate.m' generates the precision matrices and dataset corresponding to that as described in the simulation study | --> 'NExUS.m' computes the estimated partial correlation matrices corresponding to the dataset.Variable 'Partial_corr_mean' (which is a 3D array) gives the all estimated partial correlation matrices. Variable 'lambda_2_square_mean' provides the similarity index for each pair of categories | --> In case of real data, note that it is recommended to normalize the sample corresponding to each variable in the data to have mean 0 and variance 1
feature list: operation 3562
feature list: operation 3891

NG-TAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3168
citation: s13073-018-0611-9
citation: pmcid:PMC6320579
citation: pubmed:30609936
description: Next Generation-Targeted Amplicon Sequencing (NG-TAS) - an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA.
feature list: operation_0308
feature list: operation 3192
feature list: operation 3202
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Carlos Caldas's la

NGL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0099
application sub category: topic 3047
application sub category: topic 3382
citation: https://doi.org/10.1101/795161
description: CaBLAM for chiropraxis in cryoEM, UnDowser to rethink “waters”, and NGL Viewer to recapture online 3D graphics in MolProbity validation. NGL Viewer is a web application for molecular visualization. WebGL is employed to display molecules like proteins and DNA/RNA with a variety of representations.
feature list: operation_0321
feature list: operation_0337
feature list: operation 3891
license: MIT

NGLY1
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic 3474
citation: https://doi.org/10.1101/729475
description: Structured Reviews for Data and Knowledge Driven Research | The NGLY1 Deficiency Knowledge Graph | This is the repository for the NGLY1 Deficiency Knowledge Graph, the reasoning context to support hypothesis discovery for NGLY1 Deficiency-CDDG (DOID:0060728) research. The user can navigate the knowledge in the graph in the Neo4j Browser website. This knowledge graph is a structured review around the research question what is the mechanism underpinning the NGLY1-AQP1 regulation association and explaining the reduced transcriptomic expression of multiple Aquaporins in NGLY1 deficient cells?. The graph v3.2 is the first deployed in the Wikibase application for community contribution and curation

NGLess
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
citation: s40168-019-0684-8
citation: pmcid:PMC6547473
citation: pubmed:31159881
description: NGLess is a domain-specific language for NGS (next-generation sequencing data) processing with a focus on metagenomics
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: ngless.embl.de
software version: 1.0.1

NGSEA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic 3308
citation: https://doi.org/10.1101/636498
description: Network-augmented Gene Set Enrichment Analysis.
feature list: operation_0277
feature list: operation_0533
feature list: operation 2436
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial.php
primary contact: Insuk Lee

NGSEP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0625
application sub category: topic 3168
application sub category: topic 3810
citation: btz275
citation: pmcid:PMC6853766
citation: pubmed:31099384
description: NGSEP (Next Generation Sequencing Experience Platform) - accurate variant calling across species and sequencing protocols.
feature list: operation 3196
feature list: operation 3227
feature list: operation 3557
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Home
primary contact: Jorge Duitama

NGSL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3474
citation: TNNLS.2019.2944455
citation: pubmed:31689213
description: Guide Subspace Learning for Unsupervised Domain Adaptation. Guided Subspace Learning(GSL demo). In the file, there are multiple .m files. NGSL.m : Core codes of NGSL algorithm. GSL.m : Core codes of GSL algorithm.

NGSReadsTreatment
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0196
application sub category: topic 3168
application sub category: topic 3174
citation: S41598-019-48242-W
citation: pmcid:PMC6690869
citation: pubmed:31406180
description: A Cuckoo Filter-based Tool for Removing Duplicate Reads in NGS Data | NGSReadsTreatment, a computational tool for the removal of duplicated reads in paired-end or single-end datasets. NGSReadsTreatment can handle reads from any platform with the same or different sequence lengths. Using the probabilistic structure Cuckoo Filter, the redundant reads are identified and removed by comparing the reads with themselves. Thus, no prerequisite is required beyond the set of reads. NGSReadsTreatment was compared with other redundancy removal tools in analyzing different sets of reads. The results demonstrated that NGSReadsTreatment was better than the other tools in both the amount of redundancies removed and the use of computational memory for all analyses performed
feature list: operation_0290
feature list: operation 3216
feature list: operation 3564

NIPT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3056
application sub category: topic 3517
application sub category: topic 3676
citation: https://doi.org/10.1101/868588
description: Genetic profiling of 2,683 Vietnamese genomes from non-invasive prenatal testing data. VCF file of our variant call set: https://drive.google.com/file/d/1iyeuaz5w6uSVP9UyV6DjSc-GvMrYYMyr/view?usp=sharing. The analysis pipeline can be run following instructions in the Python script pipeline.py.
feature list: operation_0484
feature list: operation_0487
feature list: operation 3227

NIPTeR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0654
application sub category: topic 3168
application sub category: topic 3411
citation: s12859-018-2557-8
citation: pmcid:PMC6296037
citation: pubmed:30558531
description: R package for fast and accurate trisomy prediction in non-invasive prenatal testing.
feature list: operation 3798
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: NIPTeR.Rmd
primary contact: Lennart Johansson

NITPicker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
application sub category: topic 3678
citation: s12859-019-2717-5
citation: pmcid:PMC6444531
citation: pubmed:30940082
description: NITPicker (Next Iteration Time-point Picker) selects optimal time points (or spatial points along a single axis), that eliminates some of the biases caused by human decision-making, while maximising information about the shape of the underlying curves.
feature list: operation 3565
feature list: operation 3800
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: NITPicker
software version: 1.0.1
primary contact: Daphne Ezer

NITUMID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0108
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3518
citation: btz748
citation: pmcid:PMC8215918
citation: pubmed:31593244
description: Nonnegative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution. R package for our Nonnegative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution (NITUMID), joint work with Seyoung Park (https://sites.google.com/view/seyoungpark/home). Non-negative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution (NITUMID)
feature list: operation 2495
feature list: operation 3629
feature list: operation 3659

NJMerge
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0194
application sub category: topic_0769
citation: S13015-019-0151-X
citation: pmcid:PMC6642500
citation: pubmed:31360216
description: Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge | A tool for divide-and-conquer tree estimation via a shared distance matrix | NJMerge is a tool for scaling phylogengy estimation methods to large datasets. NJMerge can be used in a divide-and-conquer framework as follows: 1) divide the species set into disjoint subsets, 2) construct trees on each subset, and 3) combine the subset trees using an associated distance matrix (on the full species set). NJMerge has been sucessfully tested in the context of species tree estimation (Molloy and Warnow, 2018)
feature list: operation_0544
feature list: operation_0546
feature list: operation_0548

NLIMED
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic 3398
citation: https://doi.org/10.1101/756304
description: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories | This project is to convert user query to SPARQL in the Physiome Model Repository. The information looking by users usually is model entities | Natural Language Interface for Model Entity Discovery (NLIMED) is an interface to search model entities (i.e. flux of sodium across the basolateral plasma membrane, the concentration of potassium in the portion of tissue fluid) in the biosimulation models in repositories. The interface utilises the RDF inside biosimulation models and metadata from BioPortal. Currently, the interface can retrieve model entities from the Physiome Model Repository (PMR, https://models.physiomeproject.org) and the BioModels (https://www.ebi.ac.uk/biomodels/)
feature list: operation 2422
feature list: operation 3280
feature list: operation 3435

NLP ML
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0218
application sub category: topic_0634
application sub category: topic 3384
application sub category: topic 3474
citation: https://doi.org/10.1101/19012518
description: Labelling chest x-ray reports using an open-source NLP and ML tool for text data binary classification. Natural language processing and machine learning of a comma separated value (CSV) file with text data and labels. nlp_ml is a command line script that performs natural language processing and machine learning of a CSV (comma separated value) file with text data and labels. The CSV file must have the columns 'text' and 'class'. The code randomly generates classification pipelines, performs 10-fold cross validation for assessing model performance on the training dataset, and saves the results to a SQLite database. The code uses the SMOTE oversampler to avoid issues with imbalanced datasets. nlp_ml solves supervised binary classification problems using text data. When generating your CSV file, replace commas with spaces in the elements of the text column prior to saving the file.
feature list: operation 2422
license: GPL-3.0

NMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic 2828
citation: MOLECULES24183293
citation: pmcid:PMC6767145
citation: pubmed:31510014
description: Normal Mode Analysis as a Routine Part of a Structural Investigation | Webtool for Normal Mode Analysis | Web-server for Normal Mode Analysis of proteins | Are you submitting large files to WEBnma? Provide your email address in the submission box above and we will send you a link that you can visit to inspect your results when they are ready. Alternatively, you can bookmark the URL appearing in your web browser once you have submitted your job. The results can be accessed at this URL within two weeks of your submission date
feature list: operation 2476
feature list: operation 2939
feature list: operation 3891

NMF-RI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3315
application sub category: topic 3360
application sub category: topic 3382
citation: BTZ751
citation: pubmed:31593222
description: Blind spectral unmixing of highly mixed multispectral flow and image cytometry data. Matlab code to spectrally unmix highly mixed multispectral flow and image cytometry data. To use NMF-RI on new data (tissue or flow cytometry) we recommend to use the ´main.m´ code distributed and load new cytometry data to the existing folder hierarchy.
feature list: operation_0337
feature list: operation 3435
feature list: operation 3860

NMR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0099
application sub category: topic_0593
application sub category: topic 3172
citation: S41592-019-0495-7
citation: pmcid:PMC6837886
citation: pubmed:31363225
description: Single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis | In Vitro Transcription NMR. Protocol, code and examples for the co-transcriptional RNA folding network reconstruction | The protocol describes how to setup and analyse observation of a co-transcriptional RNA folding network by Systems NMR approach. While most experimental approaches can monitor only a single molecule class or reaction type at a time, Systems NMR permits single-sample dynamic quantification of entire “heterotypic” networks – involving different reaction and molecule types. It thus provides a deeper systems-level understanding of biological network dynamics by combining the dynamic resolution of biochemical assays and the multiplexing ability of “omics”
feature list: operation_0483
feature list: operation 2495
feature list: operation 3799

NMTF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic 2640
citation: https://doi.org/10.1101/739110
description: Bayesian semi-nonnegative matrix tri-factorization to identify pathways associated with cancer phenotypes | Bayesian Semi-Nonnegative Matrix Tri-Factorization | BSNMTF is a semi-nonnegative matrix tri-factorization method in the framework of Bayesian learning to identify pathways associated with cancer phenotypes (e.g., cancer sub-types or treatment outcome) from a real-valued input matrix (e.g., copy number alterations or normalized log transformed gene expression data)
feature list: operation 3501
feature list: operation 3891

NNLDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 3474
citation: FGENE.2019.00937
citation: pmcid:PMC6795129
citation: pubmed:31649723
description: Deep Learning Enables Accurate Prediction of Interplay Between lncRNA and Disease. Deep learning enables accurate prediction of interplay between lncRNA and disaeas. ###########################################################################################. NNLDA is implemented in Python 3.5 and use Tensorflow 1.12.0. Package numpy and pandas are also required. The experimental data are downloaded from LncRNADiseas2.0 database
feature list: operation 3439
feature list: operation 3625

NOCAD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3070
application sub category: topic 3407
application sub category: topic 3474
citation: F1000RESEARCH.19029.2
citation: pmcid:PMC6777013
citation: pubmed:31608146
description: Network-based Observability and Controllability Analysis of Dynamical Systems. NOCAD - Network based Observability and Controlability Analysis of Dynamical Systems toolbox for MATLAB and Octave. Daniel Leitold, Anges Vathy-Fogarassy, and Janos abonyi, NOCAD - Network based Observability and Controlability Analysis of Dynamical Systems toolbox (MATLAB version), 2017.
feature list: operation 2497

NORINE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0078
application sub category: topic 3071
application sub category: topic 3301
application sub category: topic 3307
application sub category: topic 3332
citation: s10658-018-1544-2
citation: j.synbio.2015.11.001
citation: gkm792
citation: gkv1143
citation: gkz1000
citation: https://doi.org/10.1186/1472-6807-9-15
description: NORINE is a platform that includes a database of nonribosomal peptides together with tools for their analysis.
is accessible for free: true
license: CC-BY-NC-SA-4.0

NPA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 2840
application sub category: topic 3308
citation: S12859-019-3016-X
citation: pmcid:PMC6724309
citation: pubmed:31481014
description: An R package for computing network perturbation amplitudes using gene expression data and two-layer networks | NPA - Network Perturbation Amplitude | R package and data for NPA models | The NPA (Network Perturbation Amplitude) and BIF (Biological Impact Factor) methods allow to understand the mechanisms behind and predict the effect of exposure based on transcriptomics datasets.This approach enables to translate the gene expression fold-changes into differential values for each network node, and to summarize this at the network level to provide aquantitative assessment of the degree of perturbation of the network model, the Network Perturbation Amplitude (NPA).Combining multiple relevant network models, the overall biological impact of a perturbing agent, the Biological Impact Factor (BIF),can be calculated by aggregating individual NPA scores | After package installation, networks are installed with no precomputed data
feature list: operation_0277
feature list: operation 3439
feature list: operation 3660

NPD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2269
application sub category: topic 3474
citation: https://doi.org/10.1167/19.13.17
citation: pubmed:31752016
description: The Neyman Pearson detection of microsaccades with maximum likelihood estimation of parameters. Neyman–Pearson Detector (NPD) for saccadic eye movements. By default, our algorithm reads in files X.csv and Y.csv, where the X and Y coordinates of the tracked eye-gaze positions are stored in each of the csv files. Data in the X.csv and Y.csv must be square matrices of same dimensions, and each trail of the tracked eye-gaze positions forms the rows of the input file. Our algorithm can perform the NPD on each row of the dataset independently
feature list: operation 3435
feature list: operation 3659
license: GPL-3.0

NRGXL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0176
application sub category: topic 3318
application sub category: topic 3520
citation: J.STR.2019.10.018
citation: pubmed:31753619
description: Quantitative Structural Interpretation of Protein Crosslinks. NRGXL: a tool to compute protein crosslinker conformations and energies
feature list: operation_0480
feature list: operation 2476
feature list: operation 3630

NRL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3170
application sub category: topic 3176
application sub category: topic 3295
citation: GKZ908
citation: pmcid:PMC6868436
citation: pubmed:31665434
description: CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. NRLcalc: calculation of the Nucleosome Repeat Length. The NRLcalc app provides a visual interface for the bulk calculation of the Nucleosome Repeat Length (NRL) based on multiple phasograms computed with NucTools (https://github.com/homeveg/nuctools).
feature list: operation 2575
feature list: operation 3222
feature list: operation 3659

NRStitcher
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0632
application sub category: topic 3382
citation: BTZ423
citation: pubmed:31116382
description: software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.
feature list: operation_0232
feature list: operation 3454
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Windows
software help: README.md

NSimScan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0194
application sub category: topic_0654
citation: btw126
citation: pubmed:27153714
description: DNA comparison tool with increased speed, sensitivity and accuracy.
feature list: operation 2421
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: nsimscan users guide.txt
primary contact: Denis Kaznadzey

NUFEB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0176
application sub category: topic 3697
application sub category: topic 3855
citation: https://doi.org/10.1101/648204
description: Massively Parallel Simulator for Individual-based Modelling of Microbial Communities.
feature list: operation_0337
feature list: operation 2476
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: README.md
software help: wiki
primary contact: Paolo Zuliani

NUMT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0654
application sub category: topic_0769
application sub category: topic 3168
application sub category: topic 3293
citation: S12864-019-6392-8
citation: pmcid:PMC6933719
citation: pubmed:31878873
description: Archaic mitochondrial DNA inserts in modern day nuclear genomes. Scripts used to detect archaic NUMTs in NGS data. A pipeline including a collection of scripts used to analyse NUMTs discovered in whole genome paired read data. flanking_region_analysis.py is a script used to calculate match ratios with archaic genomes of a specific genomic region. numt_stats.py is a script to calculate various statistics for discovered NUMTs. mito_variance.py is a script to calculate pariwise differences between all sequences of an alignment.
feature list: operation 3196
feature list: operation 3198
feature list: operation 3359

NUQA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2640
application sub category: topic 3168
application sub category: topic 3293
citation: msz182
citation: pmcid:PMC6878956
citation: pubmed:31424551
description: Estimating cancer spatial and temporal heterogeneity and evolution through alignment-free methods | NGS tool for Unsupervised analysis of fastQ files using Alignment-free | A software to support an alignment-free sequence comparison of large-scale fastq files using a k-mer counting methods paired with distance metrics, Jensen-Shannon divergence and Hellinger Distance | git clone https://github.com/ARoddy/NUQA.git | NUQA reads in a set of raw fastq files - ideally, these are DNA-seq files produced from multiple samples taken from the same patient. Based on these it will identify differences between the files and produce a distance matrix and a newick tree file | Eigen (where /Eigen file containing the headers is located at /usr/local/include for an example run check file 'Eigen_help.txt')
feature list: operation 3211
feature list: operation 3435
feature list: operation 3472

NaPLeS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3343
citation: S13321-019-0378-Z
citation: pmcid:PMC6688286
citation: pubmed:31399811
description: A natural products likeness scorer-web application and database | NaPLeS - Natural Product Likeness Score calculator | NaPLeS is an open source web application based fully on open data. Source and installation instructions are available at GitHub. Please submit bug reports, feature requests and general issues through the issues tracker at GitHub. NaPLeS is developed and maintained by the Steinbeck group at the University Friedrich-Schiller in Jena, Germany
feature list: operation_0337
feature list: operation 3431
feature list: operation 3803

NaS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: NaS is a hybrid approach developped to take advantage of data generated using MinION device. We combine Illumina and Oxford Nanopore technologies to produce NaS (Nanopore Synthetic-long) reads of up to 60 kb that aligned with no error to the reference genome and spanned repetitive regions.

NanoCaller
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3474
citation: https://doi.org/10.1101/2019.12.29.890418
description: NanoCaller for accurate detection of SNPs and small indels from long-read sequencing by deep neural networks. Abstract Background Variant detection from high-throughput sequencing data remains an important, unresolved yet often overlooked problem. Long-read sequencing technologies, such as Oxford Nanopore and PacBio sequencing, present unique advantages to detect SNPs and small indels in genomic regions that short-read sequencing cannot reliably examine (for example, only ∼80% of genomic regions are marked as “high-confidence region” to have SNP indel calls in the Genome In A Bottle project). However, existing software tools for short-read data perform poorly on long-read data; instead, several recent studies showed promising results in variant detection on long-read data by deep learning.
feature list: operation_0452
feature list: operation_0484
feature list: operation 3196
feature list: operation 3227
feature list: operation 3454

NanoDJ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3168
application sub category: topic 3295
citation: S12859-019-2860-Z
citation: pmcid:PMC6509807
citation: pubmed:31072312
description: Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly.
feature list: operation_0525
feature list: operation 3185
feature list: operation 3192
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: 0000-0001-5352-069X
primary contact: Marcos Colebrook

NanoDefiner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 3382
application sub category: topic 3474
citation: MA12193247
citation: pmcid:PMC6803960
citation: pubmed:31590255
description: An Implemented Decision Support Framework for Nanomaterial Identification. Official repository of the NanoDefiner e-tool for nanomaterial classification. This is the official repository for the NanoDefiner e-tool, a decision support framework for the characterisation of potential nanomaterials. It is one of the products delivered by the NanoDefine project.
feature list: operation 2428
feature list: operation 3457
license: MIT

NanoMod
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3674
citation: s12864-018-5372-8
citation: pmcid:PMC6360650
citation: pubmed:30712508
description: Computational tool to detect DNA modifications using Nanopore long-read sequencing data.
feature list: operation_0417
feature list: operation_0452
feature list: operation 3185
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: Usage.md
software version: 0.1.0
primary contact: Wang Genomics Lab

NanoPipe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0199
application sub category: topic_0781
application sub category: topic 3170
citation: giy169
citation: pmcid:PMC6377397
citation: pubmed:30689855
description: Web server for nanopore MinION sequencing data analysis.
feature list: operation_0484
feature list: operation 3185
feature list: operation 3216
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest

NanoR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
citation: journal.pone.0216471
citation: pmcid:PMC6508625
citation: pubmed:31071140
description: R package to analyze and compare nanopore sequencing data.
feature list: operation 2422
feature list: operation 3185
feature list: operation 3798
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 2.0
primary contact: Davide Bolognini

NanoSatellite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0157
application sub category: topic_0160
application sub category: topic 2885
application sub category: topic 3673
citation: S13059-019-1856-3
citation: pmcid:PMC6857246
citation: pubmed:31727106
description: Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION. Dynamic time warping of Oxford Nanopore squiggle data to characterize tandem repeats. Several tools exist to analyze tandem repeats (e.g. tandem-genotypes and RepeatHMM)
feature list: operation_0237
feature list: operation 3194
feature list: operation 3196
feature list: operation 3227
license: MIT

Nanocompore
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: https://doi.org/10.1101/843136
description: RNA modifications detection by comparative Nanopore direct RNA sequencing. RNA modifications detection from Nanopore dRNA-Seq data. Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples. Analyses performed for the nanocompore paper. Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro
feature list: operation_0417
feature list: operation_0428
feature list: operation 3196
feature list: operation 3472
license: GPL-3.0

Natural Products Atlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0218
application sub category: topic_0593
application sub category: topic 3297
application sub category: topic 3314
citation: ACSCENTSCI.9B00806
citation: pmcid:PMC6891855
citation: pubmed:31807684
description: An Open Access Knowledge Base for Microbial Natural Products Discovery. The Natural Products Atlas Network views of chemical space. The Natural Products Atlas provides a unique tools for exploring natural products chemical space, offering perspective on the position that any molecule occupies
feature list: operation 2421
feature list: operation 3216
feature list: operation 3431
feature list: operation 3803

NaviKey
type: SoftwareApplication
input: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2330
  encoding format: format 2332
output: Database search results
  type: FormalParameter
  additional type: data 2080
  encoding format: format 2330
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic 3070
application sub category: topic 3071
author: Universität Bayreuth, Department of Mycology
contributor: SNSB IT Center
description: NaviKey is a tool for querying descriptive data and has been implemented as (a) a Java applet providing the contents of DELTA files (see example with the DELTA sample data files), (b) a stand-alone Java application for accessing DELTA files or PostgreSQL versions of DiversityDescriptions databases, respectively (c) a module ("plug-in") of the Java-based Diversity Navigator database client for accessing DELTA files or PostgreSQL versions of DiversityDescriptions databases, respectively.
feature list: operation 2409
feature list: operation 2945
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: SNSB IT Center
software help: NaviKey.html
software help: www.navikey.net
software help: index.html
primary contact: Universität Bayreuth, Department of Mycology

NeOGen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3056
citation: https://doi.org/10.1111/1755-0998.12941
citation: pubmed:30194750
description: NeOGen (genetic Ne for Overlapping Generations analysis; pronounced Neo-gen) is point-&-click genetic effective population size (Ne) and demographic modelling software.
feature list: operation_0488
feature list: operation 3196
is accessible for free: true
license: GPL-3.0
operating system: Windows
software help: NeOGen-Power v1 3 0 6 a1 Guide 0 User Manual v1 1 3.pdf
software version: 1.3.0.6.a1
primary contact: J. R. Ovenden

NeSSie
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0203
citation: bty142
citation: pubmed:29522153
description: Tool for the identification of approximate DNA sequence symmetries.
feature list: operation_0239
feature list: operation 3472
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Michele Berselli

NeoFuse
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 2830
application sub category: topic 3170
application sub category: topic 3512
citation: btz879
citation: pmcid:PMC7141848
citation: pubmed:31755900
description: Predicting fusion neoantigens from RNA sequencing data. The Section for Bioinformatrics at the Biocenter of Innsbruck Medical University is commited to the generation, management, integration, and leveraging data from genomics studies. Quantification of the tumor immune contexture. Zlatko Trajanoski awarded with ERC Advanced Grant.
feature list: operation_0252
feature list: operation_0310
feature list: operation 3799
license: GPL-3.0

NeoPeptide
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0804
application sub category: topic 2640
application sub category: topic 3068
application sub category: topic 3400
citation: BAZ128
citation: pmcid:PMC6901387
citation: pubmed:31819989
description: An immunoinformatic database of T-cell-defined neoantigens. Interior-Design-Responsive-Website-Templates-Edge. NeoPeptide is a catalog of epitopes derived from neoantigens, arising from somatic mutations, captured from the literatures and immunological resources
feature list: operation_0252
feature list: operation 2421
feature list: operation 3435

NeoPredPipe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3400
citation: s12859-019-2876-4
citation: pmcid:PMC6532147
citation: pubmed:31117948
description: High-throughput neoantigen prediction and recognition potential pipeline.
feature list: operation_0487
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: README.md

NetDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0625
citation: BTZ399
citation: pubmed:31095279
description: R Package for Risk-Gene Networks.
feature list: operation 2436
feature list: operation 3439
feature list: operation 3463
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: NetDA-manual.pdf
primary contact: Minhyeok Lee

NetGO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0602
application sub category: topic 1775
application sub category: topic 3474
citation: GKZ388
citation: pmcid:PMC6602452
citation: pubmed:31106361
description: Web server that is able to improve improve large-scale protein function prediction with massive network information.
feature list: operation_0267
feature list: operation 1777
feature list: operation 3439
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: http://issubmission.sjtu.edu.cn/netgo/#
primary contact: Shanfeng Zhu
primary contact: Shuwei Yao

NetML
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3360
application sub category: topic 3512
citation: BTZ809
citation: pubmed:31688914
description: Network-based multi-task learning models for biomarker selection and cancer outcome prediction. Network-based transfer learning models for biomarker selection and cancer outcome prediction. Download eight .pk files(sample_breast_expression.pk, sample_breast_label.pk, sample_ov_expression.pk, sample_ov_label.pk, sample_PRAD.pkl, sample_PRAD_label.pkl, sample_ppi.pkl, sample_gene_names.pkl) and two .py files(NetTL_three_domains.py, NetSTL_three_domains.py) into the same fold. Run python command and execute: python3 NetTL(NetSTL)_three_domains.py The results will be exported as txt files in the same fold. sample_OV.pkl: : Ovarian Cancer gene expression data set. The size of the data is 100 x 500, 100 samples and 500 genes.
feature list: operation 2426
feature list: operation 3463
feature list: operation 3501

NetworkDataCompanion
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: https://doi.org/10.1101/2024.11.05.622163
citation: pmcid:PMC11580957
citation: pubmed:39574772
description: An R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo.

NetworkX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0605
citation: TCWV9851
description: Exploring Network Structure, Dynamics, and Function using NetworkX. Software for Complex Networks — NetworkX 3.5.1rc0.dev0 documentation. NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. It provides:. With NetworkX you can load and store networks in standard and nonstandard data formats, generate many types of random and classic networks, analyze network structure, build network models, design new network algorithms, draw networks, and much more.
feature list: operation 3891
feature list: operation 3927
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows

NeuRiPP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3474
citation: S41598-019-49764-Z
citation: pmcid:PMC6746993
citation: pubmed:31527713
description: Neural network identification of RiPP precursor peptides | NeuRiPP (Neural Network Identification of RiPP Precursor Peptides) | NeuRiPP is a neural network framework designed for classifying peptide sequences as putative precursor peptide sequences for RiPP biosynthetic gene clusters. It consists of two modules:
feature list: operation 3501
feature list: operation 3631

Neuro-Current Response Functions
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3304
application sub category: topic 3384
application sub category: topic 3444
citation: https://doi.org/10.1101/761999
description: A Unified Approach to MEG Source Analysis under the Continuous Stimuli Paradigm | The magnetoencephalography (MEG) response to continuous auditory stimuli, such as speech, is commonly described using a linear filter, the auditory temporal response function (TRF) | This repository contains the implementation of our direct TRF estimation algorithm in python (version 3.6 and above)
feature list: operation 3629
license: BSD-2-Clause

NeuroCS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3304
application sub category: topic 3474
citation: https://doi.org/10.2174/0929866526666191112150636
citation: pubmed:31721688
description: A Tool to Predict Cleavage Sites of Neuropeptide Precursors. BACKGROUND:Neuropeptides are a class of bioactive peptides produced from neuropeptide precursors through a series of extremely complex processes, mediating neuronal regulations in many aspects. Accurate identification of cleavage sites of neuropeptide precursors is of great significance for the development of neuroscience and brain science. OBJECTIVE:With the explosive growth of neuropeptide precursor data, it is pretty much needed to develop bioinformatics methods for predicting neuropeptide precursors' cleavage sites quickly and efficiently. METHOD:We started with processing the neuropeptide precursor data from SwissProt and NueoPedia into two sets of data, training dataset and testing dataset. Subsequently, six feature extraction schemes were applied to generate different feature sets and then feature selection methods were used to find the optimal feature set of each
feature list: operation_0422

NeuroChaT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 3474
application sub category: topic 3500
citation: WELLCOMEOPENRES.15533.1
description: A toolbox to analyse the dynamics of neuronal encoding in freely-behaving rodents in vivo. NeuroChaT is an open-source neuron characterisation toolbox. MNI: Original conception and design of the software architecture, primary development of algorithms and subsequent implementation in Python, primary user’s manual development, iterative development of software based on user feedback, originator of NeuroChaT acronym

NeuroMeasure
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3304
application sub category: topic 3384
application sub category: topic 3444
citation: fninf.2019.00023
citation: pmcid:PMC6499165
citation: pubmed:31105546
description: Software Package for Quantification of Cortical Motor Maps Using Frameless Stereotaxic Transcranial Magnetic Stimulation.
feature list: operation 3799
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: NeuroMeasure v4.4 User Manual.docx
software help: README.md

NeuroPP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0154
application sub category: topic_0157
application sub category: topic 3510
author: Prof. Jian Huang
citation: s12539-018-0287-2
citation: pubmed:29525981
description: Tool for the prediction of neuropeptide precursors based on optimal sequence composition.
feature list: operation_0253
feature list: operation_0418
feature list: operation 3280
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Prof. Jian Huang

NeuroPostureApp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3334
application sub category: topic 3421
citation: FNEUR.2019.01254
citation: pmcid:PMC6901659
citation: pubmed:31849818
description: The Effect of Medication and Deep Brain Stimulation on Posture in Parkinson's Disease. NeuroPostureApp©, Klinik f&uumlr Neurologie, UKSH Campus Kiel. WebApp to measure bending angle in camptocormia patients. Based on the article **to be published** from Nils Margraf and Günther Deuschl et al.
feature list: operation 3435
feature list: operation 3799

NeuroPycon
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 3304
application sub category: topic 3384
application sub category: topic 3444
citation: https://doi.org/10.1101/789842
description: A free Python toolbox for fast multi-modal and reproducible brain connectivity pipelines. Neuropycon package of functions for electrophysiology analysis, can be used from graphpype and nipype. Neuropycon — ephypype 0.1dev0 documentation. Neuropycon — graphpype 0.1dev0 documentation. Neuropycon is an open-source multi-modal brain data analysis kit which provides Python-based pipelines for advanced multi-thread processing of fMRI, MEG and EEG data, with a focus on connectivity and graph analyses. Neuropycon is based on Nipype, a tool developed in fMRI field, which facilitates data analyses by wrapping many commonly-used neuro-imaging software into a common python framework.
feature list: operation 3359
feature list: operation 3435
feature list: operation 3454

NeuroServer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic 3334
description: Standard Electroencephalography (EEG) server that mediates between the raw EEG devices and all the various EEG applications that the user may wish to run to analyse the incoming EEG data.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Windows
software help: NeuroServer
primary contact: Rudi Cilibrasi

NeuronSubtypeTranscriptomes
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3320
application sub category: topic 3512
citation: jneurosci.1615-19.2019
citation: pmcid:PMC6988999
citation: pubmed:31831521
description: Genome-wide analysis of differential gene expression and splicing in excitatory neurons and interneuron subtypes. Transcriptomics of cortical excitatory and inhibitory neurons
feature list: operation 2495
feature list: operation 2499
feature list: operation 3223
feature list: operation 3891

Neutrosophic Recommender System for Medical Diagnosis Based on Algebraic Neutrosophic Measures
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3344
application sub category: topic 3474
description: Implementation of Neutrosophic Recommender System
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0
primary contact: pham viet

New Basis Set Exchange
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3068
application sub category: topic 3314
application sub category: topic 3489
citation: ACS.JCIM.9B00725
citation: pubmed:31600445
description: An Open, Up-to-Date Resource for the Molecular Sciences Community. A repository for quantum chemistry basis sets. The new Basis Set Exchange (BSE) for Quantum Chemistry. If you are looking for the Basis Set Exchange website (which can be used to browse and download this data in a more user-friendly way), visit https://www.basissetexchange.org. This project is a library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation of basis set data. This library is used to form the backend of the new Basis Set Exchange website. A New Basis Set Exchange: An Open, Up-to-date Resource for the Molecular Sciences Community Benjamin P. Pritchard, Doaa Altarawy, Brett Didier, Tara D. Gibson, and Theresa L. Windus J. Chem. Inf. Model. 2019, 59(11), 4814-4820 doi:10.1021/acs.jcim.9b00725. A New Basis Set Exchange: An Open, Up-to-date Resource for the Molecular Sciences Community
feature list: operation 2422
feature list: operation 3283
license: BSD-3-Clause
software help: metadata

NexGenEx-Tom
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0780
application sub category: topic 3168
application sub category: topic 3308
citation: s12870-014-0412-2
citation: pmcid:PMC4340097
citation: pubmed:25849067
description: Gene Expression platform to investigate gene expression and functionalities in the tomato genome. It includes expression data from cultivated specie/variety Heinz 1706, Ailsa Craig e Solanum pimpinellifolium.
feature list: operation_0315
feature list: operation 3196
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: spot-itn-bioinfo.pdf
software version: 1
primary contact: Hamed Bostan
primary contact: Maria Luisa Chiusano

NextPolish
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0780
citation: BTZ891
citation: pubmed:31778144
description: A fast and efficient genome polishing tool for long read assembly. Fast and accurately polish the genome generated by noisy long reads. NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both. It contains two core modules, and use a stepwise fashion to correct the error bases in reference genome. To correct the raw third-generation sequencing (TGS) long reads with approximately 15-10% sequencing errors, please use NextDenovo
feature list: operation_0525
feature list: operation 3216
feature list: operation 3472

Nglyc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0130
application sub category: topic_0621
application sub category: topic_0736
application sub category: topic 2830
application sub category: topic 3474
citation: https://doi.org/10.2174/0929866526666191002111404
citation: pubmed:31577193
description: A random forest method for prediction of N-Glycosylation sites in eukaryotic protein sequence. N-Glycosylation is one of the most important post-translational mechanisms in eukaryotes. It plays a vital role in various biological processes such as protein folding, stability, immunogenicity of different proteins, cell signaling and protein targeting. N-glycosylation predominantly occurs in N-X-[S T] sequon where X is any amino acid other than proline. However, not all N-X-[S T] sequons in proteins are glycosylated. Therefore, accurate prediction of N-glycosylation sites is essential to understand N-glycosylation mechanism. We developed a random forest method, Nglyc, to predict N-glycosylation sites in eukaryotic protein sequences. The method used 315 features derived from a protein sequence and its sequence homologs. Training and testing was performed using a dataset containing 895 N-glycosylation sites and 853 non-glycosylated sites obtained from 846 PDB structures
feature list: operation_0417

NiceBot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3068
application sub category: topic 3361
application sub category: topic 3474
citation: FNBOT.2019.00076
citation: pmcid:PMC6795684
citation: pubmed:31649523
description: Inferring Continuous Subjective Ratings With Deep Regression. Data and code of the BrainLinks-BrainTools NiceBot project, manuscript "Human-Compliant Robot Behavior: Combining Continuous Subjective Evaluation with Multimodal Deep Regression Analysis".
feature list: operation 3659

NicheNet
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 2330
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
  encoding format: format 2330
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 2333
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 3308
citation: j.immuni.2019.08.017
citation: s41592-019-0667-5
citation: pmcid:PMC6876284
citation: pubmed:31561945
citation: pubmed:31819264
description: A computational method to study intercellular communication. It uses human or mouse gene expression data of interacting cells in order to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.
feature list: operation 2423
feature list: operation 2428
feature list: operation 2497
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ligand activity geneset.md
software version: 1.0.0

NimbleMiner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0218
citation: CIN.0000000000000557
citation: pubmed:31478922
description: An Open-Source Nursing-Sensitive Natural Language Processing System Based on Word Embedding | This study develops and evaluates an open-source software (called NimbleMiner) that allows clinicians to interact with word embedding models with a goal of creating lexicons of similar terms. As a case study, the system was used to identify similar terms for patient fall history from homecare visit notes (N = 1 149 586) extracted from a large US homecare agency. Several experiments with parameters of word embedding models were conducted to identify the most time-effective and high-quality model. Models with larger word window width sizes (n = 10) that present users with about 50 top potentially similar terms for each (true) term validated by the user were most effective. NimbleMiner can assist in building a thorough vocabulary of fall history terms in about 2 hours
feature list: operation 3501

Nipah
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2275
citation: https://doi.org/10.1101/623603
description: Predicting and Designing therapeutics against the Nipah virus.
feature list: operation_0482
feature list: operation 2476
feature list: operation 3899
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

NmrLineGuru
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0593
application sub category: topic_0602
application sub category: topic 3306
application sub category: topic 3336
citation: S41598-019-52451-8
citation: pmcid:PMC6831641
citation: pubmed:31690758
description: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models. Release Notes for NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis with Multi-State Equilibrium Binding Models. Please download, install, and start NmrLineGuru according to the repo page:. Before you use NmrLineGuru for your own data or project, please repeat the example simulations/fittings in the tutorials and make sure you can reproduce the example results. Feng C, Kovrigin EL, Post CB (2019) NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models. Scientific Reports 9:16023. [DOI]
feature list: operation_0244
feature list: operation 2426
feature list: operation 3799
software help: wiki

Nomogram Prognostic Model
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
application sub category: topic 2640
application sub category: topic 3379
citation: https://doi.org/10.1177/1176935119837547
citation: pmcid:PMC6452590
citation: pubmed:31057324
description: Online tool to predict the survival rate in non-small cell lung cancer patients.
feature list: operation 3557

NordScreen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2640
citation: 0284186X.2019.1615637
citation: pubmed:31106635
description: Interactive tool for presenting cervical cancer screening indicators in the Nordic countries.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Veli-Matti Partanen

NormExpression
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3518
citation: fgene.2019.00400
citation: pmcid:PMC6503164
citation: pubmed:31114611
description: Framework for researchers to select the best method for the normalization of their gene expression data based on the evaluation of different methods in the principle of the consistency of metrics and the consistency of datasets.
feature list: operation_0571
feature list: operation 3192
is accessible for free: true
license: Artistic-2.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Shan Gao

Norovirus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3305
application sub category: topic 3418
citation: S12879-019-4360-1
citation: pmcid:PMC6704660
citation: pubmed:31438883
description: Genetic diversity and epidemiology of Genogroup II noroviruses in children with acute sporadic gastroenteritis in Shanghai, China, 2012-2017 | BACKGROUND:Noroviruses (NoVs) are considered an important cause of acute gastroenteritis (AGE) across all age groups, especially in children under 5 years of age. We investigated the epidemiology of noroviruses in outpatient children from the Children's Hospital of Fudan University in Shanghai, China. METHODS:Stool specimens were collected between January 2012 and December 2017 from 1433 children under 5 years of age with acute gastroenteritis. All samples were analysed by conventional reverse transcription-polymerase chain reaction (RT-PCR) for genogroup II NoVs amplifying both the RNA-dependent RNA polymerase (RdRp) and partial capsid genes
feature list: operation_0308
feature list: operation 3196

Notch
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 2229
application sub category: topic 2830
application sub category: topic 3306
citation: RSIF.2019.0264
citation: pmcid:PMC6893490
citation: pubmed:31771451
description: Modelling cell surface dynamics and cell-cell interactions using Cell Studio. A Notch-Delta receptor binding process agent-based model using Unity 3D. The simulation was built and tested on Unity version 4.6.1, which is freely available for download at https://unity3d.com/get-unity/download/archive. To use the simulation, download the repository from GitHub, save it to a new folder (e.g. notch-delta-model), and create a project in Unity by clicking “create a new project” and select that folder (it should contain only the Assets folder and the readme file). Do not import any package. Then, load one of the scenes in the Assets folder by double clicking it.
feature list: operation_0321
feature list: operation 2426
feature list: operation 3096

Nucleome Data Bank
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0176
application sub category: topic_0621
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3656
citation: https://doi.org/10.1101/2019.12.20.885145
description: Web-based Resources to Simulate and Analyze the Three-Dimensional Genome. A web platform to simulate and browse the three-dimensional architecture of genomes. In NDB user can find data for 3D genome structures and also computational tools for simulating the genome. The server is also made for visualization the structures and dynamics of the genome, allowing users to explore the 3D organization of chromosomes from their computer. This platform enables users to visualize and annotate the 3D chromosome structures with experimental tracks from ENCODE or with their own data, allowing for an integrative experience for all genome scientists.
feature list: operation_0570
feature list: operation 2476
feature list: operation 3208

Nucleosome Dynamics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3125
application sub category: topic 3176
application sub category: topic 3308
citation: GKZ759
citation: pmcid:PMC6765203
citation: pubmed:31504766
description: A new tool for the dynamic analysis of nucleosome positioning | R package for nucleosome architecture comparison | Nucleosome Dynamics - Singularity | Nucleosome Dynamics Singularity image is a containerized implementation of 'Nucleosome Dynamics suite' | Nucleosome Dynamics Docker Container | Nucleosome Dynamics - docker implementation | This repository includes the set of R programs implementing 'Nucleosome Dynamics' analyses | Nucleosome positioning plays a major role in transcriptional regulation and most DNA-related processes | Nucleosome positioning plays a major role in transcriptional regulation DNA replication and DNA repair | R package aimed at comparing the reads of two MNase-seq experiments for nucleosome positioning and detecting significant inclusions, evictions and shifts
feature list: operation_0244
feature list: operation 3454
license: Apache-2.0

NutriGenomeDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3390
application sub category: topic 3518
citation: BAZ097
citation: pmcid:PMC6821151
citation: pubmed:31665759
description: a nutrigenomics exploratory and analytical platform. Nutrigenomics data mining platform. Nutrigenomics is defined as the science studying the role of nutrients and bioactive food compounds on gene expression. Whereas the idea of modulating human health by food intake is a millenial concept, the increasing number of research efforts on this field is pointing out that nutrition may exert its impact on health outcomes by directly affecting the expression of genes involved in critical metabolic pathways. Nowadays its widely accepted that cellular processes spanning from gene expression to protein synthesis can be regulated by dietary compounds. However there is a limited understanding of the underlying molecular mechanisms which are involved. NutriGenomeDB makes use of publicly available gene expression data obtained from nutrigenomics experiments in order to bring a the first platform for nutrigenomics data exploration
feature list: operation_0315
feature list: operation_0571
feature list: operation 2436
feature list: operation 3223

OAB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3474
citation: AOG.0000000000003517
citation: pubmed:31599833
description: Development and Validation of a Machine Learning Algorithm for Predicting Response to Anticholinergic Medications for Overactive Bladder Syndrome. Prediction of Response to Anti-Cholinergic Medication for Overactive Bladder. Number of Previously Failed Medications 0 ≥1.
feature list: operation 2428

OAC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0218
application sub category: topic 3063
application sub category: topic 3335
application sub category: topic 3400
application sub category: topic 3421
citation: https://doi.org/10.1101/19011643
citation: JOURNAL.PONE.0225625
citation: pmcid:PMC6876873
citation: pubmed:31765395
description: Semantic computational analysis of anticoagulation use in atrial fibrillation from real world data. Detect prescription of oral anticoagulants (OAC) in clinical text using regular expressions. Developed and used in Bean et al. (2019 submitted) "Semantic Computational Analysis of Anticoagulation Use in Atrial Fibrillation from Real World Data".
feature list: operation 2422
feature list: operation 2428
feature list: operation 3435

OAR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0605
application sub category: topic 2828
application sub category: topic 3314
citation: DSJ-2019-030
citation: pmcid:PMC6774380
citation: pubmed:31579260
description: Building Open Access to Research (OAR) Data Infrastructure at NIST. The NIST Open Access to Research (OAR) Public Data Repository (PDR) system software. Publishing Data Repository (oar-pdr). The oar-metadata package is a prerequisite which is configured as git sub-module of this package. This means after you clone the oar-pdr git repository, you should use git submodule to pull in the oar-metadata package into it:
feature list: operation 3435

OCMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3316
application sub category: topic 3337
citation: g3.118.200908
citation: pmcid:PMC6325911
citation: pubmed:30482799
description: Out-of-Core Matrices Analyzer (OCMA) uses state-of-the-art computational techniques that can nimbly perform eigen and Singular Value Decomposition (SVD) analyses.
feature list: operation 3196
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://github.com/precisionomics/OCMA/blob/master/OCMA_UsersManual(2018-10-14).docx
software help: README.md
software version: gamma 0.1
primary contact: Quan Long
primary contact: Zhi Xiong

OCSVM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3336
application sub category: topic 3474
citation: JOURNAL.PONE.0226115
citation: pmcid:PMC6905554
citation: pubmed:31825992
description: A novel one-class classification approach to accurately predict disease-gene association in acute myeloid leukemia cancer. Disease causing gene identification is considered as an important step towards drug design and drug discovery. In disease gene identification and classification, the main aim is to identify disease genes while identifying non-disease genes are of less or no significant. Hence, this task can be defined as a one-class classification problem. Existing machine learning methods typically take into consideration known disease genes as positive training set and unknown genes as negative samples to build a binary-class classification model. Here we propose a new One-class Classification Support Vector Machines (OCSVM) method to precisely classify candidate disease genes.
feature list: operation_0315
feature list: operation 2454

OCTAD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic_0154
application sub category: topic_0203
application sub category: topic_0208
application sub category: topic 2640
application sub category: topic 3577
citation: https://doi.org/10.1101/821546
description: An open workplace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features. All files can be found on the Chen Lab RNA-Seq server: /home/ubuntu/chenlab_v2/proj/PatrickN/desktop_pipeline_v0.1/. OCTAD:Open Cancer Therapeutic Discovery. Bin Chen, PhD. MSU. contact: Bin.Chen@hc.msu.edu. This version includes some new data files, so be sure to download those from the above directory. The pipeline is configured to run within the folder structure as found in the above directory. William Zeng. MD Candidate. UCSF. contact: billy.zeng@ucsf.edu. Please contact Patrick: patrick.newbury@hc.msu.edu with any issues. https://s3-us-west-2.amazonaws.com/chenlab-data-public/octad In the parent folder for this pipeline, create a folder named "data". Place all files from this download into this data folder. Consolidated many data files into new files: CCLE_OCTAD.RData, metadata.RData
feature list: operation 2436
feature list: operation 3223
feature list: operation 3463

OCTAVVS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0152
application sub category: topic_0593
application sub category: topic_0749
citation: https://doi.org/10.1101/2019.12.17.879387
description: A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data. Open Chemometrics Toolkit for Analysis and Visualization of Vibrational Spectroscopy data. OCTAVVS: Open Chemometrics Toolbox for Analysis and Visualization of Vibrational Spectroscopy data. OCTAVVS is a set of graphical tools for high-throughput preprocessing and analysis of vibrational spectroscopy data. Currently, the preprocessing is primarily geared towards images from infrared absorption spectroscopy with focal plane array detectors
feature list: operation_0337
feature list: operation 3432
feature list: operation 3443
license: MIT

OC_manager
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
additional type: Web application
application sub category: topic 3077
application sub category: topic 3168
application sub category: topic 3382
citation: RCM.8631
citation: pubmed:31658504
description: Open-source add-on kit for automation of zone elution in planar chromatography. Follow this link to download an image of raspbian with the OC_manager set-up, last update: 20180605. Shiny app to operate apparatus of office chromatography.
feature list: operation 3799

ODAE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Ontology
application sub category: topic_0089
application sub category: topic_0209
application sub category: topic 3399
citation: s12859-019-2729-1
citation: pmcid:PMC6509876
citation: pubmed:31074377
description: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions.
feature list: operation 3280
feature list: operation 3431
feature list: operation 3559
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Oliver He

ODAM
type: SoftwareApplication
input: Experimental measurement
  type: FormalParameter
  additional type: data 3108
  encoding format: format 3475
output: Experimental measurement
  type: FormalParameter
  additional type: data 3108
  encoding format: format 3475
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 3604
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web API
additional type: Web application
application sub category: topic_0092
application sub category: topic 3071
application sub category: topic 3473
application sub category: topic 3678
author: https://orcid.org/0000-0002-6687-7169
citation: giaa144
citation: pmcid:PMC7736789
citation: pubmed:33319910
description: ODAM (Open Data for Access and Mining) is an Experiment Data Table Management System (EDTMS) that makes research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed.
feature list: operation_0337
feature list: operation 2409
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: protocols.io.betcjeiw
software help: ODAM install VirtualBox.pdf
software help: https://app.swaggerhub.com/apis-docs/INRA-PMB/ODAM/1.2.0/
software help: ODAM
software version: 1.2
primary contact: https://orcid.org/0000-0002-6687-7169

ODNA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0219
application sub category: topic_0659
application sub category: topic 3512
citation: BAZ126
citation: pmcid:PMC6882730
citation: pubmed:31781773
description: A manually curated database of noncoding RNAs associated with orthopedics. Harbin Medical University, China
feature list: operation 2421

OG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0084
application sub category: topic_0121
application sub category: topic_0769
citation: S12859-019-2828-Z
citation: pmcid:PMC6501302
citation: pubmed:31060495
description: Consistency pipeline for hierarchies of orthologous groups (OGs) based on subsampling and tree reconciliation.
feature list: operation_0544
feature list: operation_0555
feature list: operation 3478
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: https://orcid.org/0000-0001-7734-9102

OGRDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0199
application sub category: topic_0804
application sub category: topic 3400
citation: GKZ822
citation: pubmed:31566225
description: A reference database of inferred immune receptor genes | Welcome to OGRDB - the curated Open Germline Receptor Database! | OGRDB is now accepting V- and J- sequence inferences from the human BCR light and heavy chain. Analysis scripts and submission pages have been updated accordingly
feature list: operation 3196
feature list: operation 3431

OHNOLOGS v2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0077
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic 3293
citation: gkz909
citation: pmcid:PMC7145513
citation: pubmed:31612943
description: A comprehensive resource for the genes retained from whole genome duplication in vertebrates. The code repository for OHNOLOGS v2.0 sever and multi-genome synteny comparison. A Repository of Genes Retained from Whole Genome Duplications in the Vertebrate Genomes. OHNOLOGS version 2.0 is now live with more genomes and more genome duplications!. Singh P.P. and Isambert H. (2019) OHNOLOGS v2: A comprehensive resource for the genes retained from whole genome duplication in vertebrates. Nucleic Acids Research. Singh PP & Isambert H. (2019) OHNOLOGS v2: A comprehensive resource for the genes retained from whole genome duplication in vertebrates. Nucleic Acids Research. Full text.
feature list: operation_0224
feature list: operation_0310

OLGenie
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic 3293
application sub category: topic 3697
citation: https://doi.org/10.1101/2019.12.14.876607
description: Estimating Natural Selection to Predict Functional Overlapping Genes. Program for estimating dN/dS in overlapping genes (OLGs). OLGenie is a Perl program for estimating dN/dS to detect selection and function in overlapping genes (OLGs). It relies on no external dependencies, facilitating maximum portability. Just download and run
feature list: operation_0362
feature list: operation 2454
feature list: operation 3216
license: GPL-3.0

OLOGRAM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic_0203
application sub category: topic 2269
citation: BTZ810
citation: pubmed:31688931
description: Determining significance of total overlap length between genomic regions sets. MOTIVATION:Various bioinformatics analyses provide sets of genomic coordinates of interest. Whether two such sets possess a functional relation is a frequent question. This is often determined by interpreting the statistical significance of their overlaps. However, only few existing methods consider the lengths of the overlap, and they do not provide a resolutive p-value. RESULTS:Here, we introduce OLOGRAM, which performs overlap statistics between sets of genomic regions described in BEDs or GTF. It uses Monte Carlo simulation, taking into account both the distributions of region and inter-region lengths, to fit a negative binomial model of the total overlap length. Exclusion of user-defined genomic areas during the shuffling is supported.
feature list: operation 2436
feature list: operation 3435
feature list: operation 3659
license: GPL-3.0

OMBlast
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0749
application sub category: topic 2885
citation: btw620
citation: pmcid:PMC5409310
citation: pubmed:28172448
description: Alignment tool for optical mapping using a seed-and-extend approach.
feature list: operation_0491
feature list: operation 3216
feature list: operation 3798
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Windows
software help: OMBlastManual.pdf
software help: README.md
primary contact: Kevin Y. Yip
primary contact: Ting-Fung Chan

OMH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0196
application sub category: topic 3174
citation: BTZ354
citation: pmcid:PMC6612865
citation: pubmed:31510667
description: Locality-sensitive hashing for the edit distance | We have provided the resources necceasary to generate the figures from ``Locality sensitive hashing for the edit distance'' by Guillaume Marçais, Dan DeBlasio, Prashant Pandey, and Carl Kingsford. Which is to appear inthe proceedings of ISMB/ECCB 2019 | The two main directories contain the necceasry code to produce the phylogeny figures (is_trees) and the random sequences figure (random_sequences). All of the figure generation is performed in a combination of perl and python. The omh_compute directory contains the code neccesary for the figure generation and is written in c++. This directory needs to be compiled before anything can be run in the other two
feature list: operation_0310
feature list: operation 3096

OMICfpp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3170
citation: s12864-019-5496-5
citation: pmcid:PMC6444640
citation: pubmed:30940089
description: Method for the statistical analysis of RNA-Seq paired design data.
feature list: operation 3223
feature list: operation 3436
feature list: operation 3680
is accessible for free: true

OMSSA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic 3520
citation: pubmed:15473683
description: The Open Mass Spectrometry Search Algorithm (OMSSA) is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical method used in BLAST. It is developed at the National Center for Biotechnology Information.

OMeta
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic 3174
citation: s12859-018-2580-9
description: Ontology-based, data-driven metadata tracking system.
feature list: operation 2422
feature list: operation 3352
feature list: operation 3431
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: J. Craig Venter Institute

OPA1
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0625
application sub category: topic 3334
application sub category: topic 3512
citation: S13023-019-1187-1
citation: pmcid:PMC6734442
citation: pubmed:31500643
description: 516 unique variants and 831 patients registered in an updated centralized Variome database | OPA1 (optic atrophy 1 (autosomal dominant)) | Autosomal dominant optic atrophy (DOA, Kjer type, MIM#165500) is characterized by moderate to severe loss of visual acuity with insidious onset in early childhood, blue-yellow dyschromatopsia and central scotoma
feature list: operation_0337
feature list: operation 3227
feature list: operation 3431

OPETH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3304
application sub category: topic 3421
application sub category: topic 3855
citation: https://doi.org/10.1101/783688
description: Open Source Solution for Real-time Peri-event Time Histogram Based on Open Ephys | Online Peri-Event Time Histogram for open ephys | Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them | conda create --name opeth --file requirements.txt python

OPRA
type: SoftwareApplication
input: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1476
output: Evidence
  type: FormalParameter
  additional type: data 2042
  encoding format: format 3981
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
author: http://orcid.org/0000-0001-7786-2109
author: https://orcid.org/0000-0002-7502-3157
citation: prot.22527
citation: pubmed:19714772
description: OPRA (Optimal Protein-RNA Area) is useful for identifying potential RNA-binding sites on proteins and can help to model protein-RNA interactions of biological and therapeutic interest.
feature list: operation 3902
operating system: Linux
operating system: Mac
operating system: Windows
provider: Barcelona Supercomputing Center
software help: faq and help
software help: terms

OPSCC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3407
application sub category: topic 3421
citation: S00259-019-04572-5
citation: pubmed:31720757
description: High nodal FDG uptake increases risk of distant metastasis in patients with oropharyngeal squamous cell carcinoma. BACKGROUND:The purpose of this study was to investigate if FDG uptake metrics in primary tumor and lymph node metastases in patients with oropharyngeal squamous cell carcinoma (OPSCC) has a prognostic value beyond UICC8 staging in a multiple endpoint model. METHODS:Patients with OPSCC treated with primary radiotherapy at Rigshospitalet in the period 2010-2017 were included. All patients had a pretreatment FDG PET CT scan performed. Four cause-specific Cox regression models were built for the hazard ratios (HR) of recurrence in T-, N-, M-site, and death with no evidence of disease (NED), respectively. The following variables were included: T-, N-stage, p16 status, metabolic tumor volume, and FDG uptake in both primary tumor and lymph nodes.
feature list: operation 3659

OPTIMIR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3518
citation: rna.069708.118
citation: pmcid:PMC6521604
citation: pubmed:30819774
description: Algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis.
feature list: operation_0415
feature list: operation 3196
feature list: operation 3792
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Florian Thibord

ORB-SLAM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0749
application sub category: topic 3382
citation: S19204494
citation: pmcid:PMC6832278
citation: pubmed:31623266
description: Accurate and Robust Monocular SLAM with Omnidirectional Cameras. A real-time robust monocular visual SLAM system based on ORB-SLAM for fisheye cameras, without rectifying or cropping the input images. We develop an improved monocular visual SLAM system by using omnidirectional cameras. Our method extends the ORB-SLAM2 framework with the enhanced unified camera model (EUCM) as a projection function, which can be applied to catadioptric systems and wide-angle fisheye cameras. Without rectifying or cropping the input images, the proposed system can use the full area of the images even with strong distortion.
feature list: operation 2429
feature list: operation 3435
license: GPL-3.0

ORTHOSCOPE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web service
application sub category: topic_0102
application sub category: topic 3293
application sub category: topic 3500
citation: msy226
citation: pmcid:PMC6389317
citation: pubmed:30517749
description: Automatic web tool for phylogenetically inferring bilaterian orthogroups with user-selected taxa.
feature list: operation_0544
feature list: operation_0552
feature list: operation 3478
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Jun Inoue

OSCA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0632
application sub category: topic 3172
application sub category: topic 3295
citation: s13059-019-1718-z
citation: pmcid:PMC6537380
citation: pubmed:31138268
description: OSCA (OmicS-data-based Complex trait Analysis) is a software tool for the analysis of complex traits using multi-omics data.
feature list: operation 3196
feature list: operation 3232
feature list: operation 3659
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Futao Zhang
primary contact: Jian Yang

OSTRFPD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0157
application sub category: topic_0632
application sub category: topic 2885
citation: https://doi.org/10.1177/1176934319843130
citation: pmcid:PMC6482647
citation: pubmed:31040636
description: Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer.
feature list: operation_0237
feature list: operation_0308
feature list: operation 3196
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Mallika Imwong

OSacc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0108
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3360
citation: CMAR.S215586
citation: pmcid:PMC6817837
citation: pubmed:31749633
description: Gene Expression-Based Survival Analysis Web Tool For Adrenocortical Carcinoma. Gene expression profiling data with long-term clinical follow-up information are great resources to screen, develop, evaluate and validate prognostic biomarkers in translational cancer research. However, an easy-to-use interactive online tool is needed to analyze these profiling and clinical data. In the current work, we developed OSacc (Online consensus Survival analysis of ACC), a web tool that provides rapid and user-friendly survival analysis based on seven independent transcriptomic profiles with long-term clinical follow-up information of 259 ACC patients gathered from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. OSacc allows researchers and clinicians to evaluate the prognostic value of genes of interest by Kaplan-Meier (KM) survival plot with hazard ratio (HR) and log-rank test in ACC.
feature list: operation_0337
feature list: operation 2495

OScc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2640
application sub category: topic 3360
citation: FON-2019-0412
citation: pubmed:31512935
description: An online survival analysis web server to evaluate the prognostic value of biomarkers in cervical cancer | Aim: To establish a web server that can mutually validate prognostic biomarkers of cervical cancer. Methods: Four datasets including expression profiling and relative clinical follow-up data were collected from Gene Expression Omnibus and The Cancer Genome Atlas. The web server was developed by R software. Results: The web server was named OScc including 690 patients and can be accessed at http: bioinfo.henu.edu.cn CESC CESCList.jsp. The Kaplan-Meier survival curves with log-rank p-value and hazard ratio will be generated of interested gene in OScc. Compared with previous predictive tools, OScc had the advantages of registration-free, larger sample size and subgroup analysis. Conclusion: The OScc is highly valuable to perform the preliminary assessment and validation of new or interested prognostic biomarkers for cervical cancer

OSuvm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic 3360
application sub category: topic 3379
citation: MC.23128
citation: pubmed:31646691
description: An interactive online consensus survival tool for uveal melanoma prognosis analysis. Uveal melanoma (UM) is a rare, aggressive, but the most frequent primary intraocular malignancy in adults, and up to 50% of patients develop a tendency of liver metastases. Great efforts have been made to develop biomarkers that facilitate diagnosis, prediction of the risk, and response to treatment of UM. However, a biologically informative and highly accurate gold standard system for prognostic evaluation of UM remains to be established. To facilitate assessment of the prognosis of UM patients, we established a user-friendly Online consensus Survival tool for uveal melanoma, named OSuvm, by which users can easily estimate the prognostic values of genes of interest by the Kaplan-Meier survival plot with hazard ratio and log-rank test.
feature list: operation 2495
feature list: operation 3503

OVERFRAG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic 3292
application sub category: topic 3895
citation: J.DIB.2019.103806
citation: pmcid:PMC6660583
citation: pubmed:31372451
description: An overlapping DNA fragments generator for molecular cloning and synthetic biology | Reference: Ferreira-Junior, J.R.S. ; Digiampietri, L.A. . OVERFRAG: an Overlapping Fragments Generator for Molecular Cloning and Synthetic Biology. Proceedings of the XLII Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology (SBBq), pp. 2, 2013

OakMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: Quercus robur annotation database
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 2.3

Ocean Gene Atlas
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 1929
  encoding format: format 3464
input: Gene ID
  type: FormalParameter
  additional type: data 2295
  encoding format: format 2330
input: Hidden Markov model
  type: FormalParameter
  additional type: data 1364
  encoding format: format 1370
input: Pfam accession number
  type: FormalParameter
  additional type: data 1138
  encoding format: format 2330
  encoding format: format 3464
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
  encoding format: format 3464
output: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 1929
output: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3508
  encoding format: format 3579
  encoding format: format 3603
  encoding format: format 3604
output: Ecological data
  type: FormalParameter
  additional type: data 3736
  encoding format: format 3752
output: Sequence search results
  type: FormalParameter
  additional type: data_0857
  encoding format: format 1333
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 2331
output: Phylogenetic tree
  type: FormalParameter
  additional type: data_0872
  encoding format: format 1910
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
  encoding format: format 1984
output: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0610
application sub category: topic 3174
application sub category: topic 3387
application sub category: topic 3941
citation: gky376
citation: pmcid:PMC6030836
citation: pubmed:29788376
description: The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive maps and plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.
feature list: operation_0292
feature list: operation_0567
feature list: operation_0573
feature list: operation 3478
feature list: operation 3799
funder: OCEANOMICS
is accessible for free: true
license: Not licensed
provider: MIO
software help: Ocean-Gene-Atlas User Manual.pdf
software help: termsOfUse

OdoBD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0610
application sub category: topic 3068
application sub category: topic 3489
application sub category: topic 3500
citation: https://doi.org/10.1101/804658
description: An online database for the dragonflies and damselflies of Bangladesh. Welcome to the Odonata of Bangladesh, database of the dragonflies and damselflies of Bangladesh. Situated in the South-east Asia, Bangladesh is gifted with the rich network of water resources like ponds, lakes, marshes, rivers, streams and mangrove swamps. This diverse range of water bodies along with many tropical forest patches has generated suitable habitat for many Odonata species. Till date, nearly hundred species of Odonates have been recorded from Bangladesh. The current project, supported by Rufford Small Grant, is designed to assemble and disseminate information of diversity, ecology and behavior of the Bangladeshi dragonflies and damselflies.

Odonate Phenotypic Database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0610
application sub category: topic_0625
application sub category: topic_0637
application sub category: topic 3293
application sub category: topic 3489
citation: S41597-019-0318-9
citation: pmcid:PMC6908694
citation: pubmed:31831730
description: New open data resource for comparative studies of an old insect order. The Odonate Phenotypic DataBase is a resource for dragonfly and damselfly phenotypes. The database consists of a variety of morphological, behavioural, and bio-geographical information collected from various sources. Complete Database Variable Definitions
feature list: operation_0323
feature list: operation_0326
feature list: operation 3196
feature list: operation 3431

Oligogenic resource for variant analysis (ORVAL)
type: SoftwareApplication
input: Sequence variations
  type: FormalParameter
  additional type: data 3498
  encoding format: format 3016
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0199
application sub category: topic_0622
application sub category: topic 1775
application sub category: topic 3063
application sub category: topic 3325
author: Alexandre Renaux
citation: gkz437
citation: pmcid:PMC6602484
citation: pubmed:31147699
description: ORVAL is the first web bioinformatics platform for the exploration of predicted candidate disease-causing variant combinations, aiming to aid in uncovering the causes of oligogenic diseases (i.e. diseases caused by variants in a small number of genes). This tool integrates innovative machine learning methods for combinatorial variant pathogenicity prediction, further external annotations and interactive and exploratory visualisation techniques.
feature list: operation_0331
feature list: operation 3083
feature list: operation 3439
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: Interuniversity Institute of Bioinformatics in Brussels
software help: updates
software help: documentation
software version: 3.0.0
primary contact: https://orcid.org/0000-0003-3645-1455

OliveR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3050
citation: PLANTS8090297
citation: pmcid:PMC6783963
citation: pubmed:31443503
description: High Biodiversity Arises from the Analyses of Morphometric, Biochemical and Genetic Data in Ancient Olive Trees of South of Italy | Multivariate analysis of data and geographic display of results | OliveR is an R package containing a shiny application that provides a vast series of statistical tools for exploring and analyzing both quantitative (such as morphometric or biochemical) and genetic data that can be associated to geographical coordinates. Through the use of shapefiles, the application allows visualizing both data and results of a statistical analysis directly on a geographical basis
feature list: operation 2939
feature list: operation 3196
feature list: operation 3891
license: GPL-2.0

Omic-Sig
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic 3172
citation: https://doi.org/10.1101/746123
description: Utilizing Omics Data to Explore and Visualize Kinase-Substrate Interactions | Protein phosphorylation is one of the most prevalent post-translational modifications where kinases phosphorylate their selected substrates to maintain proper signal transduction in order to regulate cellular processes. Omic-Sig is developed to stratify phospho-substrates and their associated kinases by computing and ranking the differential abundances between paired samples (e.g., Tumor and its adjacent normal tissue). The differential abundances are calculated using mass spectrometry-based phosphoproteomics and global proteomics data as well as transcriptome data from RNA-Seq. Omic-Sig also provides visualization of the computational results
feature list: operation_0417
license: Apache-2.0

OmicShare
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3360
application sub category: topic 3512
citation: PEERJ.8024
citation: pmcid:PMC6842565
citation: pubmed:31720124
description: Competing endogenous RNA (ceRNA) hypothetic model based on comprehensive analysis of long non-coding RNA expression in lung adenocarcinoma. OmicShare Tools为完全免费开放生物信息云工具网站。OmicShare Tools云平台所涵盖的生物信息基础工具全面，云平台中所有工具皆为基迪奥开发，操作简单方便，工具输出结果可直接用于SCI文章发表。. 如果您在数据处理过程中，使用了OmicShare Tools完成了分析或在OmicShare Forum得到了有价值的帮助，我们期望您在论文发表时，在方法学部分或致谢部分引用或提及OmicShare平台。例如：XXXX analysis was performed using the OmicShare tools,a free online platform for data analysis (http://www.omicshare.com/tools)。这样便于更多的同行了解和分享OmicShare平台。.
feature list: operation 2495
feature list: operation 3083
feature list: operation 3799
is accessible for free: false
license: Proprietary

OmicsARules
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0121
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3295
application sub category: topic 3512
citation: S12859-019-3171-0
citation: pmcid:PMC6839229
citation: pubmed:31703610
description: A R package for integration of multi-omics datasets via association rules mining. tool for the analysis of multimodal high-throughput data. OmicsARules is a tool for the analysis of multi-omics high-throughput data based on the use of association rules mining. OmicsARules supports to identify recurrent and associated patterns, and provides a new dimension for exploring single or multiple omics data across sequencing platforms or across samples. Besides, a new rule-interestingness measure Lamda3 is embeded in OmicsARules, it can be used to evaluate the association rules and identify biologically significant patterns. Association rule mining and visualizing were implemented in R environment using package arules and ggplot2
feature list: operation_0337
feature list: operation 2422
feature list: operation 2495

OmicsOne
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0625
application sub category: topic 3172
citation: https://doi.org/10.1101/756544
description: Associate Omics Data with Phenotypes in One-Click | a tool kit for visualization and analysis of omics data | click here or paste the repo URL:https://github.com/huizhanglab-jhu/OmicsOne.git to https://gke.mybinder.org/ as below: | Try without installation via mybinder.org
feature list: operation 2939
feature list: operation 3501
feature list: operation 3891
license: Apache-2.0

OmicsQ
type: SoftwareApplication
input: Expression data
  type: FormalParameter
  additional type: data 2603
  encoding format: format 3620
  encoding format: format 3751
output: Statistical estimate score
  type: FormalParameter
  additional type: data_0951
  encoding format: format 3752
output: Expression data
  type: FormalParameter
  additional type: data 2603
  encoding format: format 3752
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
  encoding format: format 3752
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 3508
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0602
application sub category: topic_0769
application sub category: topic 2269
application sub category: topic 3391
citation: ARXIV.2504.19813
description: OmicsQ is a Shiny-based web application designed for preprocessing and quantitative analysis of Omics data. It streamlines the preparation of data for subsequent analysis using specialized tools such as PolySTest for statistical testing and VSClust for clustering analysis.
feature list: operation_0313
feature list: operation 2238
feature list: operation 2939
feature list: operation 3435
feature list: operation 3465
feature list: operation 3799
feature list: operation 4034
is accessible for free: true
license: Apache-2.0
software help: Tutorial.pdf

OmicsX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic 3172
application sub category: topic 3174
citation: https://doi.org/10.1101/755918
description: A web server for integrated OMICS analysis | OmicsX is a user-friendly web server for integration and comparison of different omic datasets with optional sample annotation information. The tool includes four modules for gene-wise correlation, sample-wise correlation, subtype clustering, and differential expression. OmicsX provides researchers the analysis results including inter-omics correlations, conservative clusters, differential expressions, enriched biological pathways and associated phenotypes with visualization, searching, and data downloading, thus help to suggest the biological indications from the comparison of different omic data
feature list: operation 2436
feature list: operation 3891

OmniPath
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0128
citation: nmeth.4077
citation: pubmed:27898060
description: A comprehensive integrated resource of signaling pathways in activity flow representation, enzyme-substrate interactions in protein post-translational modifications, protein complexes, protein annotations and protein roles in inter-cellular signaling.
feature list: operation 3436
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

OnClass
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0089
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/810234
description: Unifying single-cell annotations based on the Cell Ontology. Single cell typing based on cell ontology. please see the document of OnClass at https://onclass.readthedocs.io/en/latest/
feature list: operation 2495
feature list: operation 3223

OnTAD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0204
application sub category: topic_0621
application sub category: topic 3169
application sub category: topic 3170
citation: S13059-019-1893-Y
citation: pmcid:PMC6918570
citation: pubmed:31847870
description: Hierarchical domain structure reveals the divergence of activity among TADs and boundaries. An Optimized Nested TAD caller for Hi-C data. OnTAD is an Optimized Nested TAD caller for Hi-C data. OnTAD <Hi-C matrix> [-penalty <float>] [-maxsz <int>] [-minsz <int>] [-ldiff <float>] [-lsize <int>] [-bedout <chrnum int> <chrlength int> <int>] [-log2] [-o output_file]
feature list: operation_0337
feature list: operation_0481
feature list: operation 3435
license: MIT

OncoLnc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3512
citation: https://doi.org/10.1155/2019/3917982
citation: pmcid:PMC6881748
citation: pubmed:31828101
description: Bioinformatics Analysis Identified Key Molecular Changes in Bladder Cancer Development and Recurrence. Here you can link TCGA survival data to mRNA, miRNA, or lncRNA expression levels. To get started simply input either a Tier 3 TCGA mRNA, miRNA, or MiTranscriptome beta lncRNA. More information can be found at this publication, youtube, or Omnes Res. News. A pan-cancer analysis using data in OncoLnc: OncoRank.
feature list: operation 2495
feature list: operation 3223
feature list: operation 3659

OncoPPi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0108
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic_0202
application sub category: topic 2640
citation: 978-1-4939-9873-9 12
citation: pubmed:31583637
description: Explore Protein-Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal. Translating Genomics Data into Protein-Protein Interaction Networks for Therapeutic Manipulation. This site provides a platform to facilitate discovery of new mechanisms to control tumorigenesis through the integration of genomic, pharmacological, clinical, and structural data with the network of cancer-associated protein-protein interactions experimentally detected in cancer cells.
feature list: operation_0276
feature list: operation 2492
feature list: operation 3083
feature list: operation 3439

OncoWiki
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0121
application sub category: topic 2640
application sub category: topic 3421
application sub category: topic 3474
application sub category: topic 3577
citation: S12909-019-1812-7
citation: pmcid:PMC6836658
citation: pubmed:31699073
description: An authentic learning approach to teaching cancer genomics. On this site you can both (a) make and upload, and (b) download and analyse simulated patient case studies.
feature list: operation 3216
feature list: operation 3283
feature list: operation 3907

OncodriveCLUSTL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2640
citation: btz588
citation: pmcid:PMC6954649
citation: pubmed:31369060
description: A sequence-based clustering method to identify cancer drivers
license: GPL-3.0

OntoKin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0154
application sub category: topic_0821
application sub category: topic 3068
application sub category: topic 3314
citation: ACS.JCIM.9B00960
citation: pubmed:31846323
description: An Ontology for Chemical Kinetic Reaction Mechanisms. A knowledge-graph built with the integration of semantic technologies and software agents for enhancing the experience of chemists in querying chemical kinetic reaction mechanisms. This User Interface (UI) demonstrates the query capability of OntoKin
feature list: operation_0224
feature list: operation 3280
feature list: operation 3454

Open-Sim Moco
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3500
citation: https://doi.org/10.1101/839381
description: Musculoskeletal optimal control. OpenSim Moco solves optimal control problems with musculoskeletal models defined in OpenSim, using direct collocation. OpenSim Moco is a software toolkit to solve optimal control problems with musculoskeletal models defined in OpenSim, including those with kinematic constraints. Using the direct collocation method, Moco can solve a wide range of problems, including motion tracking, motion prediction, and parameter optimization. The design of Moco focuses on ease-of-use, customizability, and extensibility. Just like OpenSim itself, Moco has interfaces in XML/command-line, Matlab, Python, Java, and C++.
feature list: operation 2426

Open-community Profiling Assessment tooL (OPAL)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: s13059-019-1646-y
citation: pmcid:PMC6398228
citation: pubmed:30832730
description: Tool for assessing taxonomic metagenome profilers. Implements commonly used performance metrics together with convenient visualizations.
feature list: operation_0310
feature list: operation 2495
feature list: operation 3460
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

OpenCASA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3382
citation: journal.pcbi.1006691
citation: pmcid:PMC6355034
citation: pubmed:30657753
description: Open-source and scalable computer-assisted sperm analysis (CASA) tool. Allows users to study three classical sperm quality parameters: motility, morphometry and membrane integrity (viability) and offers the possibility of analyzing the guided movement response of spermatozoa to different stimuli or different motile cells.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: Users manual v1.0.pdf
software version: 1.0

OpenCRAVAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0634
application sub category: topic_0769
application sub category: topic 2640
citation: https://doi.org/10.1101/794297
description: Open source collaborative platform for the annotation of human genetic variation. A modular annotation tool for genomic variants. Open-CRAVAT is a python package that performs genomic variant interpretation including variant impact, annotation, and scoring. It has a modular architecture with a wide variety of analysis modules that are developed both by the CRAVAT team and the broader variant analysis community. Open-CRAVAT is a product of the Karchin Lab at Johns Hopkins University in collaboration with In Silico Solutions with funding provided by the National Cancer Institute's ITCR program. Open Custom Ranked Analysis of Variants Toolkit. CRAVAT 5 is in GRCh38/hg38. If you need to annotate GRCh37/hg19 variants, check the hg19 box under Input section or use CRAVAT 4 which is in GRCh37/hg19. Documentation and Getting Started. Get started with OpenCRAVAT here or with `pip install open-cravat`.
feature list: operation_0331
feature list: operation 3226
feature list: operation 3227
license: BSD-3-Clause

OpenFlexure
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic_0634
application sub category: topic 3382
citation: https://doi.org/10.1101/861856
description: Robotic microscopy for everyone. The OpenFlexure project, which aims to make high precision mechanical positioning available to anyone with a 3D printer - for use in microscopes, micromanipulators, and more. http://openflexure.org.
feature list: operation 3443
feature list: operation 3552

OpenFmriAnalysis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3077
application sub category: topic 3384
application sub category: topic 3444
citation: JOURNAL.PONE.0223440
citation: pmcid:PMC6860425
citation: pubmed:31738777
description: Improved cortical boundary registration for locally distorted fMRI scans. An MRI analysis toolbox, primarily for laminar analysis. In order to protect your privacy, we only use cookies that are essential for the functioning of this website. Many of the functions for general fMRI preprocessing are wrappers for existing well-established neuroimaging tools. The wrappers should be seen as a consistent MATLAB command line interface to these functions, not as a reimplementation. A large part of these functions are written for my own convenience. A substantial part is new method development, mainly regarding laminar analysis. From this project root, run tvm_installLaminarAnalysisToolbox.m in MATLAB.
feature list: operation 3435
feature list: operation 3454
license: GPL-3.0

OpenProtein
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic 2814
application sub category: topic 3474
description: A PyTorch framework for tertiary protein structure prediction.
feature list: operation_0474
feature list: operation_0477
license: MIT
software version: 0.0.1

OpenSWATH
type: SoftwareApplication
input: Mass spectrometry spectra
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3246
  encoding format: format 3475
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3244
  encoding format: format 3621
  encoding format: format 3654
input: Experimental measurement
  type: FormalParameter
  additional type: data 3108
  encoding format: format 3245
  encoding format: format 3710
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3244
  encoding format: format 3621
  encoding format: format 3654
output: Peptide mass fingerprint
  type: FormalParameter
  additional type: data_0944
  encoding format: format 3475
  encoding format: format 3621
  encoding format: format 3833
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic 3520
citation: pubmed:24727770
description: OpenSWATH is a proteomics software that allows analysis of LC-MS/MS DIA (data independent acquisition) and implemented as part of OpenMS.
feature list: operation_0335
feature list: operation 3203
feature list: operation 3215
feature list: operation 3628
feature list: operation 3649
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: openswath.pdf
software version: OpenMS 2.4.0

OpenSegSPIM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3382
application sub category: topic 3500
citation: btw093
citation: pubmed:27153681
description: 3D automatic quantitative analysis tool for Single Plane Illumination Microscopy data.
feature list: operation 3629
feature list: operation 3799
is accessible for free: true
license: BSD-3-Clause
operating system: Mac
operating system: Windows
software help: faq.html
software help: opensegspim user guide.pdf
primary contact: Laurent Gole
primary contact: Sohail Ahmed
primary contact: Weimiao Yu

OpenWorm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0621
application sub category: topic 3067
application sub category: topic 3068
application sub category: topic 3300
application sub category: topic 3304
citation: peerj.preprints.1315v2
description: Unit testing, model validation, and biological simulation. Unified, simple data access python library for data & facts about C. elegans anatomy. A data access layer in Python which integrates disparate structures and representations for C. elegans anatomy and physiology. Enables a simple Python API for asking various questions about the cells of the C. elegans and enabling data sharing for the purpose of building a data-to-model pipeline for the OpenWorm project. OpenWorm is an open source project dedicated to creating a virtual C. elegans nematode in a computer. The web client of a Geppetto application. We're exploring the development of the worm via DevoWorm, an interdisciplinary project under the OpenWorm umbrella, focused on developmental processes in Nematodes and other forms of life through data analysis, visualization, and simulation.
feature list: operation 2422
feature list: operation 2426
feature list: operation 2428
license: MIT

OSSE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3325
citation: s00103-017-2536-7
citation: pubmed:28289778
description: Open Source Registry System for Rare Diseases (OSSE) - software for the creation of patient registries. Necessary interoperability between different registries is supported from the start and allows to federate those registries on a national and international level.
feature list: operation 2422
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Home
software help: Getting started v1 2.pdf
software version: 1.4
primary contact: Holger Storf

Open Targets
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0622
application sub category: topic 3053
application sub category: topic 3336
application sub category: topic 3391
description: Open Targets is a pre-competitive, public-private partnership that uses human genetics and genomics data to systematically identify and prioritise drug targets. Through large-scale genomic experiments and the development of innovative computational techniques, the partnership aims to help researchers select the best targets for the development of new therapies. At the heart of Open Targets is a consortium of complementary partner institutions that bring their respective expertise and capabilities to collaborative experimental and informatics projects. Bridging the gap between academic research and pharmaceutical drug development, Open Targets has made significant contributions to understanding the relationships between targets and diseases, established leading informatics tools in the Open Targets Platform and Open Targets Genetics, and contributed to global initiatives such as the Cancer Dependency Map.
is accessible for free: true
license: CC-BY-SA-4.0
software help: open-targets-quick-tour

Open Targets Platform
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
additional type: Web application
additional type: Web service
application sub category: topic_0085
application sub category: topic_0208
application sub category: topic 2259
application sub category: topic 3336
application sub category: topic 3342
application sub category: topic 3391
application sub category: topic 3574
citation: gkaa1027
citation: gkac1046
citation: gkw1055
citation: gky1133
citation: pmcid:PMC5210543
citation: pmcid:PMC6324073
citation: pmcid:PMC7779013
citation: pmcid:PMC9825572
citation: pubmed:27899665
citation: pubmed:30462303
citation: pubmed:33196847
citation: pubmed:36399499
description: The Open Targets Platform is a comprehensive tool that supports systematic identification and prioritisation of potential therapeutic drug targets. By integrating publicly available datasets including data generated by the Open Targets consortium, the Platform builds and scores target-disease associations to assist in drug target identification and prioritisation. It also integrates relevant annotation information about targets, diseases, phenotypes, and drugs, as well as their most relevant relationships. The Platform is a freely available resource that is actively maintained with bi-monthly updates. The data can be accessed through an intuitive web user interface, an API, Google BigQuery, and a comprehensive set of datasets available for download in JSON and Parquet formats. The pipeline and infrastructure codebases that support the Platform are open-source and can be used to create a self-hosted private instance of the Platform with custom data.
is accessible for free: true
license: Apache-2.0
software help: platform-docs.opentargets.org
software help: citation
software help: graphql-api
software help: release-notes
software help: https://www.youtube.com/watch

OptiJ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic_0196
application sub category: topic_0625
application sub category: topic 3385
application sub category: topic 3452
application sub category: topic 3794
citation: S41598-019-52065-0
citation: pmcid:PMC6821862
citation: pubmed:31666606
description: Open-source optical projection tomography of large organ samples. The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice.
feature list: operation_0337

Orbit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3382
application sub category: topic 3474
application sub category: topic 3518
citation: https://doi.org/10.1101/731000
description: An open-source whole slide image analysis tool | Orbit has many build-in image analysis algorithms. Tissue quantification using machine learning techniques, object / cell segmentation, and object classification are the basic ones. Region of interest (ROI) can be defined by manual annotations or via a trainable exclusion map. Everything can be combined | Sophisticated Image Analysis Algorithms
feature list: operation 3436
feature list: operation 3443
feature list: operation 3799
software help: help

Ordino
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 3068
citation: btz009
description: Visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples.
feature list: operation 1812
feature list: operation 3436
is accessible for free: true
license: MPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Caleydo Team

OrthoFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0091
application sub category: topic_0194
application sub category: topic_0797
application sub category: topic 3293
citation: https://doi.org/10.1101/466201
citation: s13059-015-0721-2
citation: pmcid:PMC4531804
citation: pubmed:26243257
description: OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.
feature list: operation_0324
feature list: operation_0540
feature list: operation 3182
feature list: operation 3209
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: README.md
software version: 2.0
primary contact: https://orcid.org/0000-0002-9065-8978

OrthoMCL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: 0471250953.bi0612s35
citation: gr.1224503
citation: pmcid:PMC3196566
citation: pmcid:PMC403725
citation: pubmed:12952885
citation: pubmed:21901743
description: Orthologs are homologs seperated by speciation events. Paralogs are homologs separated by duplication events. Detection of orthologs is becoming much more important with the rapid progress in genome sequencing.
feature list: operation_0553
feature list: operation 3942

OrthoVenn2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
additional type: Web service
application sub category: topic_0102
application sub category: topic_0780
application sub category: topic 3500
citation: GKZ333
citation: pmcid:PMC6602458
citation: pubmed:31053848
description: Web server for whole-genome comparison and annotation of orthologous clusters across multiple species.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: Yi Wang

OsteoporosAtlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0659
application sub category: topic 3360
application sub category: topic 3399
citation: PEERJ.6778
citation: pmcid:PMC6487800
citation: pubmed:31086734
description: Human osteoporosis-related gene database.
feature list: operation 2495
feature list: operation 3431
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Help
primary contact: Dong Li
primary contact: Yang Li

OutCyte
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0140
application sub category: topic_0154
application sub category: topic_0736
application sub category: topic_0820
application sub category: topic 3510
citation: S41598-019-55351-Z
citation: pmcid:PMC6923414
citation: pubmed:31857603
description: A novel tool for predicting unconventional protein secretion. OutCyte, as a versatile tool, can predict input proteins as signal-peptide containing, transmembrane-domain containing, intracellular or unconventionally secreted
feature list: operation_0269
feature list: operation_0418
feature list: operation 3767

OutbreakFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3168
application sub category: topic 3293
application sub category: topic 3305
citation: PEERJ.7600
citation: pmcid:PMC6717506
citation: pubmed:31523522
description: A visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling | With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial
feature list: operation_0323
feature list: operation_0552
feature list: operation_0557

P3BSseq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3168
application sub category: topic 3295
application sub category: topic 3674
citation: btw633
citation: pubmed:28172520
description: Parallel processing pipeline software for automatic analysis of bisulfite sequencing data.
feature list: operation 3186
feature list: operation 3192
feature list: operation 3359
is accessible for free: true
license: Unlicense
operating system: Linux
software help: Home
primary contact: Marcos J. Araúzo-Bravo

P3Fold
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic_0623
application sub category: topic_0736
citation: BTZ743
citation: pubmed:31584628
description: Fast and Flexible Coarse-grained Prediction of Protein Folding Routes using Ensemble Modelling and Evolutionary Sequence Variation. Predicting Protein Folding Routes.
feature list: operation_0244
feature list: operation_0303
feature list: operation_0474
feature list: operation 2415
feature list: operation 3439

PACES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0108
application sub category: topic 3474
application sub category: topic 3512
citation: S41598-019-47594-7
citation: pmcid:PMC6668381
citation: pubmed:31366994
description: Prediction of N4-acetylcytidine (ac4C) modification sites in mRNA | prediction of acetylation sites in mRNA | PACESPrediction of ac4C(N4-acetylcytidine) sites in mRNA | Citation:Zhao W., Zhou Y., Cui Q. & Zhou Y. PACES: prediction of N4-acetylcytidine (ac4C) modification sites in mRNA. Sci Rep 9, 11112, doi:10.1038/s41598-019-47594-7 (2019)
feature list: operation_0417
feature list: operation 2495
feature list: operation 3431

PACKMAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic_0209
application sub category: topic_0821
citation: j.jmb.2019.11.018
citation: pmcid:PMC7029793
citation: pubmed:31786268
description: Characterizing and Predicting Protein Hinges for Mechanistic Insight. PACKMAN: PACKing and Motion ANalysis
feature list: operation_0244
feature list: operation 1843
feature list: operation 2476

PACKMOL-Memgen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0153
application sub category: topic_0769
application sub category: topic_0820
citation: ACS.JCIM.9B00269
citation: pubmed:31120747
description: Generalized workflow for automated building of membrane-protein-lipid-bilayer systems based on open-source tools including Packmol, memembed, pdbremix, and AmberTools.
feature list: operation_0417
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Amber19.pdf

PADMet
type: SoftwareApplication
input: Pathway or network
  type: FormalParameter
  additional type: data 2600
  encoding format: format 1637
  encoding format: format 2585
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0092
application sub category: topic_0602
author: Méziane Aite
citation: https://doi.org/10.1101/462556
citation: journal.pcbi.1006146
citation: antiox8110564
citation: pmcid:PMC5988327
citation: pmcid:PMC6912245
citation: pubmed:29791443
citation: pubmed:31744163
description: Portable Database for Metabolism. It is a format to centralizes, in a new graph-based PADMet, all information about a metabolic network. It also provides methods to import, to update, to analyse and to export data, in a library.
feature list: operation 2409
feature list: operation 3927
feature list: operation 3928
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: padmet.readthedocs.io

PADS Arsenal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0621
application sub category: topic_0623
application sub category: topic_0654
application sub category: topic 3292
application sub category: topic 3489
citation: gkz916
citation: pmcid:PMC7145686
citation: pubmed:31620779
description: A database of prokaryotic defense systems related genes. Procaryotic Antiviral Defense System. procaryotic database, defense system database, pangenome database. PADS Arsenal A Database of Prokaryotic Defense Systems Related Genes.
feature list: operation_0337
feature list: operation_0435
feature list: operation 2422

PAFScaff
type: SoftwareApplication
input: Sequence assembly
  type: FormalParameter
  additional type: data_0925
  encoding format: format 1929
output: Sequence assembly
  type: FormalParameter
  additional type: data_0925
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0622
author: https://orcid.org/0000-0002-3645-5539
citation: zenodo.3707027
description: PAFScaff (Pairwise mApping Format reference-based scaffold anchoring and super-scaffolding) is designed for mapping genome assembly scaffolds to a closely-related chromosome-level reference genome assembly. It uses (or runs) Minimap2 to perform an efficient (if rough) all- against-all mapping, then parses the output to assign assembly scaffolds to reference chromosomes.
feature list: operation_0523
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: pafscaff
software version: v0.2.1
primary contact: https://orcid.org/0000-0002-3645-5539

PAGE-Net
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3382
application sub category: topic 3474
citation: pubmed:31797610
description: Interpretable and Integrative Deep Learning for Survival Analysis Using Histopathological Images and Genomic Data. A biologically interpretable integrative deep learning model that integrates PAthological images and GEnomic data. PAGE_net_pretrain : code for pretraining and saving the pretrained model. Integration of aggregated pathological images and genomic data
feature list: operation 3436

PAMOGK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3047
citation: https://doi.org/10.1101/834168
description: A Pathway Graph Kernel based Multi-Omics Clustering Approach for Discovering Cancer Patient Subgroups. Install dependencies: if using virtual env omit --user parts. pip install -r requirements.txt --user. For mosek set environment variable MOSEKLM_LICENSE_FILE to your license file install mosek package with
feature list: operation 3432
feature list: operation 3436
feature list: operation 3454

PANDA-view
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2269
citation: bty408
citation: pmcid:PMC6184437
citation: pubmed:29790911
description: Tool for statistical analysis and visualization of quantitative proteomics data
feature list: operation 2939
feature list: operation 3557
feature list: operation 3799
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: download
primary contact: Cheng Chang
primary contact: Yunping Zhu

PANPASCO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 3305
application sub category: topic 3321
application sub category: topic 3324
application sub category: topic 3673
citation: JOURNAL.PCBI.1007527
citation: pmcid:PMC6922483
citation: pubmed:31815935
description: Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters. Next-generation sequencing based base-by-base distance measures have become an integral complement to epidemiological investigation of infectious disease outbreaks. This study introduces PANPASCO, a computational pan-genome mapping based, pairwise distance method that is highly sensitive to differences between cases, even when located in regions of lineage specific reference genomes. We show that our approach is superior to previously published methods in several datasets and across different Mycobacterium tuberculosis lineages, as its characteristics allow the comparison of a high number of diverse samples in one analysis-a scenario that becomes more and more likely with the increased usage of whole-genome sequencing in transmission surveillance
feature list: operation_0484
feature list: operation 3198
feature list: operation 3227
feature list: operation 3432

PARC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2229
application sub category: topic 3306
citation: https://doi.org/10.1101/765628
description: Ultrafast and accurate clustering of phenotypic data of millions of single cells | PARC, “phenotyping by accelerated refined community-partitioning” - is a fast, automated, combinatorial graph-based clustering approach that integrates hierarchical graph construction (HNSW) and data-driven graph-pruning with the new Leiden community-detection algorithm
feature list: operation 3557
feature list: operation 3891
license: MIT

PASA
type: SoftwareApplication
input: Alignment
  type: FormalParameter
  additional type: data 1916
input: Keyword
  type: FormalParameter
  additional type: data_0968
input: Gene report
  type: FormalParameter
  additional type: data_0916
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic_0621
description: Program to Assemble Spliced Alignment. PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.
feature list: operation_0232
feature list: operation_0310

PASCCA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 3512
application sub category: topic 3518
citation: s12864-019-5433-7
citation: pmcid:PMC6343338
citation: pubmed:30669970
description: R package for analyses of alternative polyadenylation (APA) related gene expression, including the characterization of poly(A) sites, quantification of association between genes with/without repeated measurements, clustering of APA-related genes to infer significant APA specific gene modules, and the evaluation of clustering performance with a variety of indexes.
feature list: operation_0313
feature list: operation 2495
feature list: operation 3766
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software version: 0.1.0
primary contact: Wenbin Ye
primary contact: Yuqi Long

PASER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3304
application sub category: topic 3384
application sub category: topic 3444
citation: https://doi.org/10.1101/739409
description: PASER for automated analysis of neural signals recorded in pulsating magnetic fields | PASER: Processing and Analysis Schemes for Extracellular Recordings | Currently, PASER can only be used with data saved by Open Ephys GUI [Ref. 4], specifically .continuous files. See https://github.com/open-ephys/plugin-GUI or http://www.open-ephys.org/ for more information
feature list: operation 3891
license: BSD-3-Clause

PASNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic 3360
application sub category: topic 3407
citation: s12859-018-2500-z
citation: pmcid:PMC6296065
citation: pubmed:30558539
description: Pathway-associated sparse deep neural network for prognosis prediction from high-throughput data.
feature list: operation_0277
feature list: operation 3439
feature list: operation 3557
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md

PASTEClassifier
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0157
author: URGI
citation: journal.pone.0091929
citation: pmcid:PMC4008368
citation: pubmed:24786468
contributor: URGI
description: The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features. It browses the whole spectrum of possible classifications at order level using Wicker hierarchical system. It is also able to automatically classify other repeated elements like SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. The output is designed to facilitate manual curation by providing to the biologist all characteristics that have been found on each TE sequence.
is accessible for free: true
license: CECILL-2.0
operating system: Linux
operating system: Mac
provider: URGI
software help: PASTEClassifier-tuto
software version: 2.0

PASTMUS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0154
application sub category: topic_0769
application sub category: topic 2640
application sub category: topic 3168
citation: S13059-019-1897-7
citation: pmcid:PMC6913009
citation: pubmed:31842968
description: Mapping functional elements at single amino acid resolution in human cells. Identification of functional elements for a protein of interest is important for achieving a mechanistic understanding. However, it remains cumbersome to assess each and every amino acid of a given protein in relevance to its functional significance. Here, we report a strategy, PArsing fragmented DNA Sequences from CRISPR Tiling MUtagenesis Screening (PASTMUS), which provides a streamlined workflow and a bioinformatics pipeline to identify critical amino acids of proteins in their native biological contexts. Using this approach, we map six proteins-three bacterial toxin receptors and three cancer drug targets, and acquire their corresponding functional maps at amino acid resolution
feature list: operation_0321
feature list: operation 1812
feature list: operation 2429
feature list: operation 3096
feature list: operation 3767

PASeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0781
citation: pmcid:PMC6736041
description: A10 Presence and frequency of M184V mutation in the MOBIDIP trial | AbstractThe MOBIDIP trial evaluated the simplification by protease (PI r) monotherapy for HIV infection versus dual therapy and boosted protease inhibitor plus lamivudine (PI r + 3TC) in controlled patients under second-line regimens. MOBIDIP was interrupted because of a significant number of patients with virological failure (VF) at week 48 (W48) in PI r (33 133, ∼25%) versus in PI r + 3TC (4 132, ∼3%). At the time of first-line VF, 96 per cent of patients harbored the M184V mutation. The presence of the M184V mutation was related to a protective effect against VF in the PI r + 3TC arm. We developed a methodology that allows to determine the frequency of M184V I mutations in the HIV reverse transcriptase (RT) gene in peripheral blood mononuclear cells (PBMC) obtained before MOBIDIP simplification

PATHcrosstalk
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3360
citation: J.EBIOM.2019.05.010
citation: pmcid:PMC6606892
citation: pubmed:31101593
description: R package for crosstalk correction in Pathway Deregulation Score (PDS) inferred by Pathifier algorithm.
feature list: operation_0487
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Botao Fa
primary contact: Zhangsheng Yu

PATOPA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic 2269
application sub category: topic 2640
application sub category: topic 3676
citation: S12859-019-3218-2
citation: pmcid:PMC6889196
citation: pubmed:31791231
description: A probabilistic method for leveraging functional annotations to enhance estimation of the temporal order of pathway mutations during carcinogenesis. “rectal_table”: All the nonsynonymous mutations in TCGA rectal cancer dataset and its coresponding Polyphen-2 scores. The first column is the sample names, the second column is the mutated genes and the third column is the functional impact score corresponding to each mutations. “CoreGroup2Gene.txt”: contains the mapping of pathways to genes (genes entrez id). The first column is the name of pathways, the second column is genes included in the pathways. The file "example1.R” is an example of R codes which read the data file “rectal_table” and “CoreGroup2Gene.txt” and analyze the 9 pathways in “CoreGroup2Gene.txt” together. The file returns “pairprob.txt” which contains the probabilities of A>B, A<B and A=B for all pairs of pathways.
feature list: operation_0533
feature list: operation 3083
feature list: operation 3562

PAVFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3360
application sub category: topic 3512
citation: btz902
citation: pmcid:PMC7141844
citation: pubmed:31790154
description: Fusion detection in assembled transcriptomes. Post-Assembly Variant Finder (PAVFinder). PAVFinder is a Python package that detects structural variants from de novo assemblies (e.g. ABySS, Trans-ABySS). As such, it is able to analyse both genome and transcriptome assemblies:.
feature list: operation_0524
feature list: operation 3227
feature list: operation 3258

PBWT-Query
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3337
citation: BTZ347
citation: pmcid:PMC6612857
citation: pubmed:31510689
description: Efficient haplotype matching between a query and a panel for genealogical search | Efficient haplotype matching between a query and panel using PBWT-Query | Ardalan Naseri, Erwin Holzhauser, Degui Zhi, Shaojie Zhang
feature list: operation_0487
feature list: operation 2421
feature list: operation 3211

PCA-PAM50
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3518
citation: S41598-019-44339-4
citation: pmcid:PMC6538748
citation: pubmed:31138829
description: Principle Component Analysis-based iterative PAM50 subtyping (PCA-PAM50) improves consistency between breast cancer intrinsic and clinical subtyping reclassifying a subset of luminal A tumors as luminal B.
feature list: operation 2939
feature list: operation 3891
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Praveen K. Raj Kumar

PCAViz
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0176
application sub category: topic_0602
application sub category: topic 2828
citation: ACS.JCIM.9B00703
citation: pmcid:PMC6849643
citation: pubmed:31580061
description: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser. PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing molecular dynamics trajectories via a web browser. PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing MD trajectories via a web browser. To encourage use, an easy-to-install PCAViz-powered WordPress plugin enables 'plug-and-play' trajectory visualization. Jacob Durrant software July 29, 2019September 30, 2019
feature list: operation 1812
feature list: operation 2476
feature list: operation 2939
feature list: operation 3890
feature list: operation 3891

PCHi-C
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0749
application sub category: topic 3170
application sub category: topic 3179
application sub category: topic 3315
citation: S12859-019-3237-Z
citation: pmcid:PMC6933681
citation: pubmed:31881819
description: Topological structure analysis of chromatin interaction networks. Analysis and visualisation tools for PCHi-C interaction networks
feature list: operation_0276
feature list: operation_0277
feature list: operation 3083
license: GPL-3.0

PCIR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0780
application sub category: topic 3293
application sub category: topic 3360
application sub category: topic 3810
citation: BAZ127
citation: pmcid:PMC6835207
citation: pubmed:31696928
description: A database of Plant Chloroplast Inverted Repeats. Plant Chloroplast Inverted Repeats. Welcome to PCIR! Plant Chloroplast Inverted Repeats (PCIR) is an interactive, web-based platform containing various sequenced chloroplast genomes that enables detection, searching, and visualization of large-scale detailed information on IRs. PCIR contains many datasets, including 21,433 IRs, 113 plants chloroplast genomes, 16,948 functional genes and 21,659 visual maps. This database offers an online prediction tool for detecting IRs based on Chloroplast DNA sequences. PCIR can also analyze phylogenetic relationships using IR information among different species and provide users with high-quality marker maps. This database will be a valuable resource for IR distribution patterns, related genes and architectural features
feature list: operation_0282
feature list: operation_0337
feature list: operation 2421

PCMBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic_0625
application sub category: topic 2269
application sub category: topic 3293
citation: J.TPB.2019.11.005
citation: pubmed:31805292
description: Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts. An R-package for specification, simulation and likelihood calculation of phylogenetic comparative models. PCMBase : Simulation and likelihood calculation of phylogenetic comparative methods. Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree.
feature list: operation_0323
feature list: operation_0326
feature list: operation_0567
feature list: operation 3891

PCOSBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0089
application sub category: topic_0121
application sub category: topic_0219
application sub category: topic_0602
application sub category: topic_0634
citation: BAX098
citation: pubmed:31725861
description: A manually curated database of polycystic ovarian syndrome. Nor Afiqah-Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein, PCOSBase: a manually curated database of polycystic ovarian syndrome, Database, Volume 2017, 2017, bax098
feature list: operation 2421
feature list: operation 2422
feature list: operation 3431
feature list: operation 3439

PDBUSQLExtractor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0097
citation: molecules24010179
citation: pmcid:PMC6337464
citation: pubmed:30621295
description: Scalable Extraction of Big Macromolecular Data in Azure Data Lake Environment.
feature list: operation_0224
feature list: operation_0279
feature list: operation 1812
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: repo-PDBUSQLExtractor
primary contact: D. Mrozek

PDEparams
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
citation: https://doi.org/10.1101/631226
description: Parameter fitting toolbox for partial differential equations in Python.
feature list: operation_0337
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Esteban A. Hernandez-Vargas

PDGA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3047
application sub category: topic 3056
application sub category: topic 3336
citation: CHEMRXIV.10247567.V1
description: Populating Chemical Space with Peptides using a Genetic Algorithm. In drug discovery one uses chemical space as a concept to organize molecules according to their structures and properties. One often would like to generate new possible molecules at a specific location in chemical space marked by a molecule of interest. Herein we report the peptide design genetic algorithm (PDGA, code available at https: github.com reymondgroup PeptideDesignGA), a computational tool capable of producing peptide sequences of various chain topologies (linear, cyclic polycyclic or dendritic) in proximity of any molecule of interest in a chemical space defined by MXFP, an atom-pair fingerprint describing molecular shape and pharmacophores. We show that PDGA generates high similarity analogs of bioactive peptides, including in selected cases known active analogs, as well as of non-peptide targets.

PEATmoss
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0203
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3382
application sub category: topic 3518
citation: TPJ.14607
citation: pubmed:31714620
description: A unified gene expression atlas for the model plant Physcomitrella patens. PEATmoss is an interactive tool to visualize gene expression data. These help pages explain several ways to query the expression data and to visualize the results, enabling the comparison of the expression profiles of several genes simultaneously, as well as to visualize co-expression information. One section describes how to download the expression data in a format that is easy to export to spreadsheet software and to generate figures that are ready for presentations or publications.
feature list: operation_0224
feature list: operation_0315
feature list: operation_0571
software help: help

PEFF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic 3520
citation: ACS.JPROTEOME.9B00064
citation: https://doi.org/10.1101/624494
citation: pmcid:PMC6642660
citation: pubmed:31081335
description: PSI Extended Fasta Format (PEFF) is a proposed unified format for protein and nucleotide sequence databases to be used by sequence search engines and other associated tools.
feature list: operation_0335
feature list: operation_0417
feature list: operation 3645
is accessible for free: true
license: Apache-2.0
operating system: Windows
software help: TestExample Windows.txt
primary contact: https://orcid.org/0000-0001-8732-0928

PELE-MSM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic_0602
application sub category: topic 3315
application sub category: topic 3375
citation: ACS.JCTC.9B00753
citation: pubmed:31589430
description: PELE-MSM is a Monte Carlo Based Protocol for the Estimation of Absolute Binding Free Energies. IIt is a fully automatic platform based on our Monte Carlo algorithm, the Protein Energy Landscape Exploration method (PELE), for the estimation of absolute protein-ligand binding free energies, one of the most significant challenges in computer-aided drug design. Based on a ligand pathway approach, an initial short enhanced sampling simulation is performed to identify reasonable starting positions for more extended sampling. This stepwise approach allows for a significantly faster convergence of the free energy estimation using the Markov State Model (MSM) technique. PELE-MSM was applied on four diverse protein and ligand systems, successfully ranking compounds for two systems. Based on the results, current limitations and challenges with physics-based methods in computational structural biology are discussed.
feature list: operation_0482
feature list: operation 2476
feature list: operation 3896
software help: msm pele

PEMA
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
  encoding format: format 1931
output: Biodiversity data
  type: FormalParameter
  additional type: data 3707
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic 3050
description: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes
feature list: operation 3200
is accessible for free: true
license: GPL-3.0
software help: https://docs.google.com/presentation/d/1lVH23DPa2NDNBhVvOTRoip8mraw8zfw8VQwbK4vkB1U/edit

PER viewer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0623
application sub category: topic_0634
citation: https://doi.org/10.1101/641043
description: Identification of pathogenic variant enriched regions across genes and gene families.
feature list: operation 3225
feature list: operation 3227
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: tab-6062-4
software help: tab-6062-5
primary contact: Dennis Lal
primary contact: Eduardo Pérez-Palma

PERs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0623
application sub category: topic_0634
application sub category: topic 3120
application sub category: topic 3168
citation: gr.252601.119
citation: pmcid:PMC6961572
citation: pubmed:31871067
description: PERs is a tool for Identification of pathogenic variant enriched regions across genes and gene families.
feature list: operation 3225
feature list: operation 3226
feature list: operation 3227
license: MIT

PFOND
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic 3063
application sub category: topic 3325
citation: resprot.2675
citation: pmcid:PMC3742411
citation: pubmed:23920006
description: Portal for Families Overcoming Neurodevelopmental Disorders (PFOND) provides a structured web interface for the information sharing with individuals struggling with the consequences of rare developmental disorders.
feature list: operation 3431
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Wasserman Lab

PGConverter
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3827
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3247
  encoding format: format 3684
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3247
  encoding format: format 3681
  encoding format: format 3684
  encoding format: format 3827
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3247
  encoding format: format 3681
  encoding format: format 3684
  encoding format: format 3827
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3247
  encoding format: format 3681
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3247
  encoding format: format 3681
  encoding format: format 3684
  encoding format: format 3827
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3827
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3681
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3004
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3247
  encoding format: format 3681
  encoding format: format 3684
  encoding format: format 3827
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0121
application sub category: topic 3071
application sub category: topic 3520
description: This library is primarily to offer a command-line tool to convert between the following formats for proteogenomics related data. It is also possible to convert regular non-proteogenomics mzIdentML or PRIDE XML files to mzTab. A secondary function of this library is to gather metadata and statistics about mzIdentML, mzTab, and PRIDE XML files for validation purposes. Primarily this tool is powered by the ms-data-core-api library to read/write files. Primarily this tool is powered by the ms-data-core-api library to read/write files.
feature list: operation_0335
feature list: operation_0336
feature list: operation 1812
feature list: operation 2409
feature list: operation 2422
feature list: operation 3695
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: PGConverter
software version: 1.8.5

PGG Han
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3056
application sub category: topic 3517
application sub category: topic 3673
citation: gkz829
citation: pmcid:PMC6943055
citation: pubmed:31584086
description: The Han Chinese Genomes Database (PGG.Han) serves as the central repository of the genomic data of the Han Chinese Genomes Project (Phase I). As is its current version, PGG.Han archives genomic data of 114,783 Han Chinese individuals (a.k.a. Han100K), including high coverage WGS data (n = 319), low coverage WGS data (n = 11878), and high-density SNV data with 8,056,973 variants genotyped or partially imputed (n = 102,586. PGG.Han aims to facilitate: 1) population structure analysis; 2) ancestry inference; 3) imputation; 4) GWAS. Computational tools are implemented into the PGG.Han, and an online user interface is provided for data analysis and results visualization.
feature list: operation_0484
feature list: operation 3196
feature list: operation 3454
feature list: operation 3557
feature list: operation 3791

PGG SNV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic 2815
application sub category: topic 3056
application sub category: topic 3796
citation: S13059-019-1838-5
citation: pmcid:PMC6805450
citation: pubmed:31640808
description: PGG SNV is a database for understanding evolutionary and medical implications of human single nucleotide variations in diverse populations. The tool provides useful web tools for figure illustration. Users can upload their local files with specific format (see readme and example at the top-right corner of each tool) generated by their own analysis to draw their figures as well as download them. The current version includes tools on (a) heatmap plot of population differentiation; (b) word map plot of allele frequency distributions; (c) manhattan plot of natural selection signals; and (d) heatmap plot for linkage disequilibrium analysis.
feature list: operation_0488
feature list: operation 2421
feature list: operation 3196
feature list: operation 3211
feature list: operation 3227

PGP-UK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3170
application sub category: topic 3173
application sub category: topic 3308
application sub category: topic 3518
application sub category: topic 3577
citation: S41597-019-0205-4
citation: pmcid:PMC6823446
citation: pubmed:31672996
description: PGP-UK is an open access resource of human multi-omics data.
feature list: operation 2428
feature list: operation 2495
feature list: operation 3227

PGP_tools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
description: Manipulation,filter and sort NGS data.

PGxLOD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0208
application sub category: topic 3068
description: PGxLOD is intended to host pharmacogenomic knowledge that the PractiKPharma project will extract from various sources such as the literature and Electronic Health Records.

PGxMine
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0208
application sub category: topic_0218
application sub category: topic 3375
application sub category: topic 3474
application sub category: topic 3577
citation: pmcid:PMC6917032
citation: pubmed:31797632
description: This is the codebase for the PGxMine project to using text-mining to identify papers for curation into PharmGKB. It is a Python3 project that makes use of the Kindred relation classifier along with the PubRunner project to run tools across PubMed and accessible PubMed Central.
feature list: operation_0306
feature list: operation 1812
feature list: operation 3675
license: MIT

PHAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3168
citation: bty1003
citation: pubmed:30561651
description: Pathogen–Host Analysis Tool (PHAT) is an application for processing and analyzing next-generation sequencing (NGS) data as it relates to relationships between pathogens and their hosts.
feature list: operation 3196
feature list: operation 3218
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Windows
software help: PHATDocs
software version: 0.10.1-beta.1
primary contact: Chris Gibb

PHENO
type: SoftwareApplication
output: Genotype/phenotype report
  type: FormalParameter
  additional type: data_0920
  encoding format: format 3749
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0625
citation: btz190
citation: pmcid:PMC6792114
citation: pubmed:30903186
description: PHENO aims to provide access to plant phenotypic datasets, with a major focus on the woody plant domain. Plant phenotyping is central to plant research and breeding and is becoming increasingly throughput, with large amounts of data being generated from diverse experimental settings. Access to phenotypic datasets annotated according to widely accepted standards contributes for data interoperability, enabling powerful genotype-phenotype association studies.
feature list: operation 2429
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: brapi.org
software version: 1.3

PHENOSTAMP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0625
application sub category: topic 2259
application sub category: topic 2640
application sub category: topic 3474
citation: S41467-019-13441-6
citation: pmcid:PMC6898514
citation: pubmed:31811131
description: PHENOtypic STAte MaP (PHENOSTAMP) is an algorithm that combines the Clustering Classification and sorting Tree(CCAST) algorithm (Anchang et al. 2014) with an optimal 2D visualization of projected single-cell data using a neural network. It is mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution.
feature list: operation 2429
feature list: operation 3802
feature list: operation 3891

PHG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3810
citation: https://doi.org/10.1101/775221
description: Practical Haplotype Graph (PHG) facilitates genome-wide imputation and cost-effective genomic prediction. Successful management and utilization of increasingly large genomic datasets are essential for breeding programs to increase genetic gain and accelerate cultivar development. To help with data management and storage, a sorghum Practical Haplotype Graph (PHG) pangenome database stores all identified haplotypes and variant information for a given set of individuals.
feature list: operation_0484
feature list: operation_0487
feature list: operation 3196
feature list: operation 3211
feature list: operation 3557

PHI-Nets
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0621
application sub category: topic_0625
application sub category: topic_0659
application sub category: topic_0780
citation: FMICB.2019.02721
citation: pmcid:PMC6908471
citation: pubmed:31866958
description: PHI-Nets is a network resource for Ascomycete fungal pathogens to annotate and identify putative virulence interacting proteins and siRNAs.
feature list: operation_0276
feature list: operation 2492
feature list: operation 3439
feature list: operation 3461
license: MIT

PHOSforUS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0160
application sub category: topic_0605
application sub category: topic 3306
citation: https://doi.org/10.1101/866558
description: PHOSforUS is a fully biophysical parameter-based protein phosphorylation site predictor.
feature list: operation_0303
feature list: operation_0417
feature list: operation 3891
license: MIT

PHYLOViZ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic_0084
citation: s13015-017-0119-7
citation: pmcid:PMC5815242
citation: pubmed:29467814
description: Scalable data integration and visualization for multiple phylogenetic inference methods.
feature list: operation_0337
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorials.html
software help: latest

PICEAdatabase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0625
application sub category: topic 3308
citation: BAZ089
citation: pmcid:PMC6694207
citation: pubmed:31414118
description: PICEAdatabase is a web database for Picea omics and phenotypic information.
feature list: operation 3639

PIMENTo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic_0769
application sub category: topic 3518
citation: 978-1-4939-9004-7 11
citation: pubmed:30649727
description: Pipeline for Integrated Microarray Expression Normalization Tool kit (PIMENTo) for tumor microarray profiling experiments.
feature list: operation 2428
feature list: operation 2495
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: man
software version: 1.0
primary contact: Thomas Nash

PINOT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0128
application sub category: topic 3063
application sub category: topic 3068
citation: https://doi.org/10.1101/788000
description: PINOT is a Protein Interaction Network Online Tool.
feature list: operation_0276
feature list: operation 2492
feature list: operation 3083
software version: 1.1

PINSPlus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0634
application sub category: topic 3295
application sub category: topic 3384
citation: bty1049
citation: pubmed:30590381
description: Tool for tumor subtype discovery in integrated genomic data.
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: PINSPlus.pdf
software version: 2.0.0
primary contact: Hung Nguyen

PIPE-T
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3308
application sub category: topic 3360
application sub category: topic 3518
application sub category: topic 3519
citation: S41598-019-53155-9
citation: pmcid:PMC6879478
citation: pubmed:31772190
description: PIPE-T is a Galaxy Workflow for processing and analyzing miR expression profiles by RTqPCR. It is a tool that offers several state-of-the-art options for parsing, filtering, normalizing, imputing and analyzing RT-qPCR expression data. Integration of PIPE-T into Galaxy allows experimentalists with strong bioinformatic background, as well as those without any programming or development expertise, to perform complex analysis in a simple to use, transparent, accessible, reproducible, and user-friendly environment
feature list: operation 1812
feature list: operation 3435
feature list: operation 3557
feature list: operation 3799
feature list: operation 3891
license: MIT

PIPPA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic_0780
description: PSB Interface for plant phenotype analysis
feature list: operation 2940
feature list: operation 3695
operating system: Linux
software version: 0.14.20

PIPR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic 3474
citation: BTZ328
citation: pmcid:PMC6681469
citation: pubmed:31510705
description: PIPR is a multifaceted protein-protein interaction prediction based on Siamese residual RCNN.
feature list: operation_0272
feature list: operation_0480
feature list: operation 2492

PIRATE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0114
application sub category: topic_0199
application sub category: topic_0623
application sub category: topic_0625
application sub category: topic 3168
citation: GIZ119
citation: pmcid:PMC6785682
citation: pubmed:31598686
description: PIRATE is a fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria.
feature list: operation 3359
feature list: operation 3431
feature list: operation 3432
license: GPL-3.0

PIRCh-seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic 3179
application sub category: topic 3295
application sub category: topic 3512
citation: S13059-019-1880-3
citation: pmcid:PMC6924075
citation: pubmed:31862000
description: This tool contains scripts for PIRCh-seq. It provides a pipeline for functional classification of non-coding RNAs associated with distinct histone modifications
feature list: operation 2436
feature list: operation 2441
feature list: operation 3222

PIRD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2830
application sub category: topic 3400
citation: BTZ614
citation: pubmed:31373607
description: Pan immune repertoire database (PIRD) collects raw and processed sequences of immunoglobulins (IGs) and T cell receptors (TCRs) of human and other vertebrate species with different phenotypes. You can check the detailed information of each sample in the database, choose samples to analyze according to your need, and upload data to analyze. Your analysis results will be auto-saved, so you can return to check them at any time.
feature list: operation_0337
feature list: operation 2422
feature list: operation 3431

PIZSA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0128
application sub category: topic_0130
application sub category: topic 2275
citation: GKZ368
citation: pmcid:PMC6602501
citation: pubmed:31114890
description: Protein Interaction Z-Score Assessment.
feature list: operation_0272
feature list: operation_0321
feature list: operation 2492
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: faq.html
primary contact: M. S. Madhusudhan

PK-DB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2840
application sub category: topic 3375
application sub category: topic 3379
citation: https://doi.org/10.1101/760884
description: PK-DB is a database and web interface for pharmacokinetics data and information from clinical trials as well as pre-clinical research. PK-DB allows to curate pharmacokinetics data integrated with the corresponding meta-information
feature list: operation 3196
feature list: operation 3435

PLACNETw
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0102
application sub category: topic_0196
citation: btx462
citation: pubmed:29036591
description: Web-based tool for plasmid reconstruction from bacterial genomes.
feature list: operation 3195
feature list: operation 3198
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: placnetw video
software help: README.md
primary contact: Fernando de la Cruz

PLUMED
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0176
application sub category: topic_0749
application sub category: topic 3314
citation: S41592-019-0506-8
citation: pubmed:31363226
description: Promoting transparency and reproducibility in enhanced molecular simulations | The public repository of the PLUMED consortium | PLUMED-NEST is the public repository of the PLUMED consortium. It provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation (or analysis) contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual | The community-developed PLUgin for MolEcular Dynamics | PLUMED is an open-source, community-developed library that provides a wide range of different methods, which include: | Home News People Download Doc Forum Cite NEST Funding
feature list: operation_0244
feature list: operation 2476

PMBD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0218
application sub category: topic_0821
application sub category: topic 3297
application sub category: topic 3489
application sub category: topic 3697
citation: BAZ119
citation: pmcid:PMC6859810
citation: pubmed:31738435
description: PMBD is a Comprehensive Plastics Microbial Biodegradation Database.
feature list: operation_0305

PMD-FDR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0769
application sub category: topic 3512
application sub category: topic 3520
citation: https://doi.org/10.1101/839290
description: PMD-FDR is a Robust and Reproducible Statistical Framework for Removing Low-Accuracy, High-Scoring Hits.
feature list: operation 2929
feature list: operation 3216
feature list: operation 3644
feature list: operation 3645
feature list: operation 3649

PMMLogit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2269
application sub category: topic 2830
citation: https://doi.org/10.1101/778472
description: High-dimensional Bayesian phenotype classification and model selection using genomic predictors.
feature list: operation 3659

PN-BOTTM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0605
application sub category: topic 2640
application sub category: topic 3421
citation: s00520-019-04837-7
citation: pmcid:PMC6954125
citation: pubmed:31073852
description: Patient Navigation Barriers and Outcomes Tool™ (PN-BOT™), a new information management and reporting tool for oncology PN programs.
feature list: operation 3454
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: PNBOT Quick Start Guide.pdf
primary contact: Mandi Pratt-Chapman

PNC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic 2640
application sub category: topic 3577
citation: JOURNAL.PCBI.1007520
citation: pmcid:PMC6901264
citation: pubmed:31765387
description: The PNC package is to identify personalized driver genes of an individual patient by using network control principle .
feature list: operation_0277
feature list: operation 2454
feature list: operation 3223
feature list: operation 3439
feature list: operation 3463

PNV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3050
application sub category: topic 3306
application sub category: topic 3474
citation: PEERJ.PREPRINTS.26811V2
description: PNV is an assessment of Machine Learning algorithms for estimating land potential.
feature list: operation 2429
feature list: operation 3431
feature list: operation 3659
license: GPL-3.0

PORGY
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 3292
application sub category: topic 3855
citation: 978-1-4939-9102-0 3
citation: pubmed:30945242
description: Interactive visual environment for rule-based modelling of biochemical systems.
feature list: operation_0337
feature list: operation 3216
feature list: operation 3431
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: porgy doc.zip
primary contact: Bruno Pinaud
primary contact: Guy Melancon

PPCheck
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0130
application sub category: topic 2275
citation: MINF.201800145
citation: pubmed:31535472
description: PPCheck is a bioinformatics tool to identify protein-protein interactions, predict hotspots, perform compuational alanine scanning, predict native-like docking pose and calculate residue conservation for a protein.
feature list: operation_0394
feature list: operation 2492
feature list: operation 3899

PPHAGE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0114
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3474
application sub category: topic 3517
citation: S12864-019-6140-0
citation: pmcid:PMC6842548
citation: pubmed:31706268
description: Genome-wide prediction and prioritization of human aging genes by data fusion.
feature list: operation 2454
feature list: operation 3439
feature list: operation 3501

PPICurator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic_0218
citation: pmic.201800291
citation: pubmed:30521143
description: Tool for extracting comprehensive protein-protein interaction information.
feature list: operation_0306
feature list: operation 2421
feature list: operation 2492
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help

PPNID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0769
application sub category: topic 3810
citation: BTZ707
citation: pubmed:31529041
description: PPNID: a manually curated reference database and identification tool for plant-parasitic nematode.
license: GPL-3.0
software help: Tutorial.pdf

PPP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0769
application sub category: topic 3796
citation: https://doi.org/10.1101/785774
description: A Software Platform for Facilitating Population Genomic Analyses. Installation — PPP 0.1.1 documentation. Free document hosting provided by Read the Docs
feature list: operation_0335
feature list: operation 3435

PPR-SSM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic_0625
application sub category: topic 3382
application sub category: topic 3473
citation: S12859-019-3157-Y
citation: pmcid:PMC6819326
citation: pubmed:31664891
description: personalized PageRank and semantic similarity measures for entity linking. BACKGROUND:Biomedical literature concerns a wide range of concepts, requiring controlled vocabularies to maintain a consistent terminology across different research groups. However, as new concepts are introduced, biomedical literature is prone to ambiguity, specifically in fields that are advancing more rapidly, for example, drug design and development. Entity linking is a text mining task that aims at linking entities mentioned in the literature to concepts in a knowledge base. For example, entity linking can help finding all documents that mention the same concept and improve relation extraction methods. Existing approaches focus on the local similarity of each entity and the global coherence of all entities in a document, but do not take into account the semantics of the domain. RESULTS:We propose a method, PPR-SSM, to link entities found in documents to concepts from domain-specific ontologies
feature list: operation 3096
feature list: operation 3280
feature list: operation 3625
feature list: operation 3778

PPSBoost
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0081
application sub category: topic_0601
application sub category: topic 3474
citation: PROT.25801
citation: pubmed:31412138
description: Boosting phosphorylation site prediction with sequence feature-based machine learning | Index of /~pralay/resources/PPSBoost | Shyantani Maiti, Atif Hassan, Pralay Mitra (In press). Boosting phosphorylation site prediction with sequence feature-based Machine learning. PROTEINS: Structure, Function, and Bioinformatics
feature list: operation_0417

PPV NPV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3305
application sub category: topic 3360
citation: S41512-017-0017-Y
citation: pmcid:PMC6460848
citation: pubmed:31093546
description: Novel method for interrogating receiver operating characteristic curves for assessing prognostic tests.
feature list: operation_0337
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-8734-7335

PPanGGOLiN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0621
application sub category: topic_0623
application sub category: topic 3174
application sub category: topic 3305
citation: https://doi.org/10.1101/836239
description: PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species
feature list: operation_0310
feature list: operation_0362
feature list: operation 3797
feature list: operation 3891

PQStat
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 2269
application sub category: topic 3305
citation: GH.2019.791
citation: pubmed:31724381
description: PQStat is an application which enables users to carry out a statistical data analysis in a simple and accurate way.
feature list: operation 3432
feature list: operation 3658
feature list: operation 3891

PRALINE 2
type: SoftwareApplication
input: Nucleic acid sequence record
  type: FormalParameter
  additional type: data 2887
  encoding format: format 1929
input: Protein sequence record
  type: FormalParameter
  additional type: data 2886
  encoding format: format 1929
output: Profile-profile alignment
  type: FormalParameter
  additional type: data_0868
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0080
author: https://orcid.org/0000-0002-7971-6209
description: PRALINE 2 is a framework for tailor-made sequence alignments. It allows almost all aspects of a sequence alignment algorithm to be customised, such as the alphabets used (AA, DNA, secondary structure, disorder, motif matches, etc.). Includes a command-line tool for common use cases without writing any custom code.
feature list: operation_0492
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
software version: 1.0.0
software version: 1.1.0
primary contact: Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit

PRAM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: https://doi.org/10.1101/636282
description: Pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments.
feature list: operation_0264
feature list: operation 3680
feature list: operation 3800
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: pram.pdf
software help: README.md
primary contact: Peng Liu

PRAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3512
application sub category: topic 3794
citation: JOURNAL.PCBI.1007227
citation: pmcid:PMC6716675
citation: pubmed:31425505
description: > HOMEPAGE BROKEN! | Predicting functional targets of RNA binding proteins based on CLIP-seq peaks | RNA-protein interaction plays important roles in post-transcriptional regulation. Recent advancements in cross-linking and immunoprecipitation followed by sequencing (CLIP-seq) technologies make it possible to detect the binding peaks of a given RNA binding protein (RBP) at transcriptome scale. However, it is still challenging to predict the functional consequences of RBP binding peaks. In this study, we propose the Protein-RNA Association Strength (PRAS), which integrates the intensities and positions of the binding peaks of RBPs for functional mRNA targets prediction. We illustrate the superiority of PRAS over existing approaches on predicting the functional targets of two related but divergent CELF (CUGBP, ELAV-like factor) RBPs in mouse brain and muscle
feature list: operation 3222
feature list: operation 3901
feature list: operation 3902

PRECOG: Predicting coupling probabilities of G-protein coupled receptors
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2330
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3307
citation: gkz392
citation: pmcid:PMC6602504
citation: pubmed:31143927
description: PRECOG (Predicting coupling probabilities of G-protein coupled receptors) lets you predict coupling probabilities of Class A GPCRs to 11 G-proteins based on input sequence information (either WT or mutated). It is built by training logistic-regression algorithm on sequence- and structure-based features, derived from a set of Class A GPCRs.
feature list: operation_0337
feature list: operation 2423
feature list: operation 2990
operating system: Linux
operating system: Mac
software version: 1.1

PRIGSA2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0157
application sub category: topic_0623
application sub category: topic_0749
application sub category: topic_0820
application sub category: topic 2814
citation: https://doi.org/10.1101/803304
description: Improved version of Protein Repeat Identification by Graph Spectral Analysis. Protein Repeat Identification by Graph Spectral Analysis. PRIGSA2 is a graph based algorithm which implements knowledge-based and de novo approach for the identification of structural repeats in proteins. The tool takes PDB file as input and gives the periodicity and coordinates as output
feature list: operation_0245
feature list: operation_0267
feature list: operation_0303
feature list: operation_0476
feature list: operation 3214

PRIMEval
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0632
application sub category: topic 3518
application sub category: topic 3519
application sub category: topic 3673
citation: S41598-019-55883-4
citation: pmcid:PMC6917790
citation: pubmed:31848453
description: PRIMEval is a tool for optimization and screening of multiplex oligonucleotide assays.
feature list: operation 2419
feature list: operation 2428
feature list: operation 3198
license: MIT

PRINCESS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3263
application sub category: topic 3325
citation: btw758
citation: pmcid:PMC5860394
citation: pubmed:28065902
description: Privacy-preserving international collaboration framework for analyzing rare disease genetic data that are distributed across different continents.
feature list: operation 3196
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
primary contact: Feng Chen

PRISM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3674
citation: BTZ327
citation: pmcid:PMC6612819
citation: pubmed:31510697
description: > NAME EQUAL TO (PUB. DIFFERENT) bio.tools/prism-ppi | > NAME (PRISM) SIMILAR TO (PUB. DIFFERENT) bio.tools/prism_3 (PRISM 3), bio.tools/prism-primer (PriSM), bio.tools/prism (PrISM) | methylation pattern-based, reference-free inference of subclonal makeup | Methylation Pattern-based, Reference-free Inference of Subclonal Makeup. (v1.0.1) | PRISM requires the mapping result of Bismark, a bisulfite read mapping tool. Also note that PRISM only applies to RRBS data, and unfortunately, the feasibility of PRISM to the data from other methylation profiling techniques such as whole genome bisulfite sequencing (WGBS), methylated DNA immunoprecipitation sequencing (MeDIP-Seq), or methyl-CpG binding domain-based capture sequencing (MBDCap-Seq) has not been verified | BAM file of RRBS reads, aligned by Bismark
feature list: operation 3186
feature list: operation 3206
feature list: operation 3629
license: MIT

PRODIGY-LIG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
additional type: Web service
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic 2275
author: http://orcid.org/0000-0001-7369-1322
citation: BTY816
citation: pubmed:31051038
description: Large-scale prediction of binding affinity in protein-small ligand complexes.
feature list: operation_0272
feature list: operation_0482
feature list: operation 2492
funder: European H2020 e-Infrastructure grant, BioExcel, grant no. 675728
funder: European H2020 e-Infrastructure grant, BioExcel, grant no. 823830
funder: European H2020 e-Infrastructure grant, EOSC-Hub, grant no.777536
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: http://orcid.org/0000-0001-7369-1322
provider: University of Utrecht
software help: README.md
software help: manual

PRODIGY-CRYSTAL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0128
application sub category: topic_0196
application sub category: topic 1317
application sub category: topic 2828
citation: btz437
citation: pmcid:PMC9186318
citation: pubmed:31141126
description: PRODIGY-CRYSTAL (PROtein binDIng enerGY prediction to classify CRYSTALlographic interfaces) is an automatic web server for distinguish crystallographic from biological interfaces in protein complexes.
feature list: operation_0321
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: heading c three
primary contact: http://orcid.org/0000-0001-7369-1322
primary contact: Anna Vangone

PROMO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3360
citation: https://doi.org/10.1101/629584
description: PROMO (Profiler of Multi-Omics data) - interactive tool for analyzing clinically-labeled multi-omic cancer datasets.
feature list: operation 3501
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: PROMO Example Tutorial.htm
primary contact: Dvir Netanely
primary contact: Ron Shamir

PRP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3295
citation: BAZ130
citation: pmcid:PMC6891001
citation: pubmed:31796964
description: PRP is a comprehensive integrated regulatory information and analysis portal for plant genomes. Gene regulation is a highly complex and networked phenomenon where multiple tiers of control determine the cell state in a spatio-temporal manner. Among these, the transcription factors, DNA and histone modifications, and post-transcriptional control by small RNAs like miRNAs serve as major regulators. An understanding of the integrative and spatio-temporal impact of these regulatory factors can provide better insights into the state of a 'cell system'. Yet, there are limited resources available to this effect. Therefore, we hereby report an integrative information portal (Plant Regulomics Portal; PRP) for plants for the first time.
feature list: operation 1781
feature list: operation 3083
feature list: operation 3207
feature list: operation 3792

PRRpred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2830
application sub category: topic 3400
application sub category: topic 3473
application sub category: topic 3474
citation: https://doi.org/10.1101/846469
description: A Hybrid Model for Predicting Pattern Recognition Receptors using Evolutionary Information. Prediction of pattern recognition receptors. PRRpred is a web server designed for predicting pattern Recognition Receptors (PRRs) and Non-PRRs
feature list: operation_0267
feature list: operation_0416
feature list: operation 2489

PRS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3298
application sub category: topic 3416
application sub category: topic 3517
citation: https://doi.org/10.1101/467910
description: Atlas of polygenic burden associations across the human phenome.
feature list: operation_0484
feature list: operation 3196
feature list: operation 3435
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-7918-2040

PReMiS
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3244
  encoding format: format 3710
  encoding format: format 3712
output: Quality control report
  type: FormalParameter
  additional type: data 3914
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
description: PReMiS analyzes mass spectrometric data collected from the 6×5 LC-MS/MS Peptide Reference Mix and calculates quality control metrics for instrument performance. Thermo raw files and AB Sciex wiff files can be analyzed directly. Data in other vendor formats must be converted to mzML prior to analysis. In addition to its general reporting features, PReMiSallows you to track performance over time and compare parameters across instruments.
feature list: operation 3635
is accessible for free: true
license: Proprietary
operating system: Windows

PS-Plant
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0780
application sub category: topic 3382
application sub category: topic 3474
citation: GIZ056
citation: pmcid:PMC6534809
citation: pubmed:31127811
description: Photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: https://www.youtube.com/watch
primary contact: 0000-0002-7255-872X

PSCP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic 2814
application sub category: topic 3534
citation: PEERJ.PREPRINTS.27743
description: Protein Structural Class Prediction.
feature list: operation_0474
feature list: operation_0482
feature list: operation 2575
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Swakkhar Shatabda

PSI-Sigma
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3512
citation: btz438
citation: pmcid:PMC6901072
citation: pubmed:31135034
description: Splicing-detection method for short-read and long-read RNA-seq analysis.
feature list: operation 3680
feature list: operation 3798
feature list: operation 3800
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Kuan-Ting Lin

PSI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic 3168
citation: BTZ341
citation: pmcid:PMC6612829
citation: pubmed:31510650
description: Fully-sensitive seed finding in sequence graphs using a hybrid index | Graph REad Mapper (C++ implementation) | Google protocol buffer >= v3.0.0
feature list: operation_0249
feature list: operation_0524
feature list: operation 3211
license: MIT

PSMD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0632
application sub category: topic 2640
application sub category: topic 2885
application sub category: topic 3489
application sub category: topic 3810
citation: https://doi.org/10.1111/1755-0998.13098
citation: pubmed:31599098
description: An extensive database for pan-species microsatellite investigation and marker development. A Django app for Pan-Species Microsatellite Database. Pan-Species Microsatellite Database. Microsatellites (simple repeat sequences, SSRs or short tandem repeats, STRs), are tandem repeats of short DNA motifs with length of 1-6 bp which have extensively been exploited as powerful genetic markers for diversity applications, and are involved in gene regulation as well as implicated in numerous genetic diseases even in cancers. PSMD was developed as a web-based comprehensive database comprising 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms covered almost all species with available genomic data. PSMD enables scientists to easily browse, filter, compare, download SSRs with relevant information
feature list: operation_0237
feature list: operation_0308
feature list: operation 2421
feature list: operation 3196
license: MIT

PSPer
type: SoftwareApplication
input: Protein sequence (raw)
  type: FormalParameter
  additional type: data 2974
  encoding format: format 1929
output: Protein features
  type: FormalParameter
  additional type: data 1277
  encoding format: format 3464
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: btz274
citation: pubmed:30994888
description: Prediction of FUS-like phase separation proteins
feature list: operation 3092
primary contact: https://orcid.org/0000-0001-7470-4324

PSRN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0659
application sub category: topic_0780
application sub category: topic 3170
citation: s12864-018-5367-5
citation: pmcid:PMC6307140
citation: pubmed:30587128
description: Plant stress RNA-Seq nexus (PSRN) - stress-specific transcriptome database in plant cells.
feature list: operation 3223
feature list: operation 3680
feature list: operation 3800
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: syslab5.nchu.edu.tw
primary contact: Systems Biology Lab, National Chung Hsing University

PSSRdt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: GENES10110917
citation: pmcid:PMC6895799
citation: pubmed:31717904
description: PSSRdt is a novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data.
feature list: operation_0237
feature list: operation_0308
feature list: operation_0524
feature list: operation 3196
feature list: operation 3258

PTM-CrossTalkMapper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0203
application sub category: topic_0601
application sub category: topic 3295
application sub category: topic 3520
citation: j.ymeth.2020.01.012
description: Visualization of the Dynamics of Histone Modifications and Their Crosstalk Using PTM-CrossTalkMapper. R scripts to create crosstalk maps that visualize multi-layered proteoform data. PTM-CrossTalkMapper is a flexible toolkit to visualize multi-layered quantitative post-transcriptional modification (PTM) data. The preprint manuscript can be found on bioRxiv
feature list: operation_0337
feature list: operation_0417
feature list: operation 3755
feature list: operation 3799
software help: documentation
software help: 978-1-0716-2317-6 13

PTMphinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic 3520
citation: peerj.7046
citation: pmcid:PMC6555389
citation: pubmed:31198645
description: R package for PTM site localization and motif extraction from proteomic datasets.
feature list: operation_0335
feature list: operation_0417
feature list: operation 3755
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 0.1.0
primary contact: Jacob M. Wozniak

PTR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic 2640
citation: pubmed:31797620
description: PTR is an approach to identify and explore Post Transcriptional Regulatory mechanisms using proteogenomics.
feature list: operation 3431

PTRBC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3403
application sub category: topic 3421
application sub category: topic 3474
citation: https://doi.org/10.1101/19008045
description: PTRBC is a tool for predicting the required pre-surgery blood volume in surgical patients based on machine learning. This clinical data analysis tool can be used to do data cleaning and predict the required transfusion volume of red blood cells in surgical patients based on machine learning methods. Meanwhile, this tool can process the similar classification or regression problems. In other words, a general prediction model can be established for the input data specified.
feature list: operation 3435
feature list: operation 3659

PTWAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2269
application sub category: topic 3170
application sub category: topic 3337
application sub category: topic 3517
citation: https://doi.org/10.1101/808295
description: Investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis. Probabilistic Transcriptome-wide Association Analysis (PTWAS). This repository contains the software implementations and necessary annotation resources for a suite of statistical methods to perform transcriptome-wide association analysis (TWAS). These methods are designed to perform rigorous causal inference connecting genes to complex traits. The statistical models and the key algorithms are described in the manuscript [1]
feature list: operation 3196
feature list: operation 3232
feature list: operation 3659
feature list: operation 3664
feature list: operation 3891

PUG-View
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 2840
application sub category: topic 3314
citation: S13321-019-0375-2
citation: pmcid:PMC6688265
citation: pubmed:31399858
description: programmatic access to chemical annotations integrated in PubChem | PubChem is a chemical data repository that provides comprehensive information on various chemical entities. It contains a wealth of chemical information from hundreds of data sources. Programmatic access to this large amount of data provides researchers with new opportunities for data-intensive research. PubChem provides several programmatic access routes. One of these is PUG-View, which is a Representational State Transfer (REST)-style web service interface specialized for accessing annotation data contained in PubChem. The present paper describes various aspects of PUG-View, including the scope of data accessible through PUG-View, the syntax for formulating a PUG-View request URL, the difference of PUG-View from other web service interfaces in PubChem, and its limitations and usage policies
feature list: operation_0337
feature list: operation 2422
feature list: operation 3431

PVCTools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0780
application sub category: topic 2259
application sub category: topic 3168
application sub category: topic 3308
citation: J.HELIYON.2019.E02530
citation: pmcid:PMC6812194
citation: pubmed:31667383
description: parallel variation calling tools. PVCTools is Parallel Variation Calling Tools, which tries to call variation using multiple threads. Basically, the reference genome will be splited into small pieces, and corresponding alignment BAM files will be extracted. Under this way, it will speed up the process of variation calling a lot
feature list: operation 3359
feature list: operation 3432

PXS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3063
application sub category: topic 3337
application sub category: topic 3577
citation: https://doi.org/10.1101/833632
description: Poly-Exposure and Poly-Genomic Scores Implicate Prominent Roles of Non-Genetic and Demographic Factors in Four Common Diseases in the UK. ABSTRACT While polygenic risk scores (PRSs) have been shown to identify a small number of individuals with increased clinical risk for several common diseases, non-genetic factors that change during a lifetime, such as lifestyle, employment, diet, and pollution, have a larger role in clinical prediction. We analyzed data from 459,613 participants of the UK Biobank to investigate the independent and combined roles of demographics (e.g., sex and age), 96 environmental exposures, and common genetic variants in atrial fibrillation, coronary artery disease, inflammatory bowel disease, and type 2 diabetes. We develop an additive modelling approach to estimate and validate a poly-exposure score (PXS) that goes beyond consideration of a handful of factors such as smoking and pollution
feature list: operation 3196
feature list: operation 3659

PYLFIRE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 2269
application sub category: topic 3056
citation: WELLCOMEOPENRES.15583.1
description: Python implementation of likelihood-free inference by ratio estimation. Likelihood-Free Inference by Ratio Estimation (LFIRE). PYLFIRE is a Python package that uses ELFI (Engine for Likelihood-Free Inference) and glmnet for performing Likelihood-Free Inference. PYLFIRE requires Python 3.6 or greater and a Fortran compiler, for Mac users brew install gcc will take care of this requirement or conda install gcc if you are using anaconda. You can install PYLFIRE by typing in your terminal:
feature list: operation 3658
feature list: operation 3659
feature list: operation 3664

PYRO-NN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3384
application sub category: topic 3452
application sub category: topic 3474
citation: mp.13753
citation: pmcid:PMC6899669
citation: pubmed:31389023
description: Python reconstruction operators in neural networks | Python Reconstruction Operators in Neural Networks. High level python API for PYRO-NN-Layers | Implementation of reconstruction operators in CUDA for Tensorflow for the PYRO-NN Framework | Python Reconstruction Operators in Machine Learning (PYRO-NN-Layers) brings state-of-the-art reconstruction algorithms to neural networks integrated into Tensorflow. This repository contains the actual Layer implementation as CUDA kernels and the necessary C++ information control classes according to the Tensorflow API | At this point the geometry is fully setup and can be used to create projections and reconstructions
feature list: operation_0487
feature list: operation 3660
feature list: operation 3745
license: Apache-2.0

PaCBAM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic 3577
application sub category: topic 3676
citation: S12864-019-6386-6
citation: pmcid:PMC6933905
citation: pubmed:31878881
description: Fast and scalable processing of whole exome and targeted sequencing data. PaCBAM_Performance_analysis – Google Drev
feature list: operation 2422
feature list: operation 3227
feature list: operation 3695

PaSGAL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2885
application sub category: topic 3315
application sub category: topic 3512
citation: https://doi.org/10.1101/651638
description: PaSGAL (Parallel Sequence to Graph Aligner) is designed to accelerate local sequence alignment of sequences to directed acyclic sequence graphs (DAGs), e.g., variation graphs, splicing graphs.
feature list: operation_0495
feature list: operation 3196
feature list: operation 3198
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Haowen Zhang
primary contact: Srinivas Aluru

PaWFE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3318
application sub category: topic 3474
citation: FNBOT.2019.00074
citation: pmcid:PMC6746931
citation: pubmed:31551749
description: Fast Signal Feature Extraction Using Parallel Time Windows | Motivation: Hand amputations can dramatically affect the quality of life of a person. Researchers are developing surface electromyography and machine learning solutions to control dexterous and robotic prosthetic hands, however long computational times can slow down this process. Objective: This paper aims at creating a fast signal feature extraction algorithm that can extract widely used features and allow researchers to easily add new ones. Methods: PaWFE (Parallel Window Feature Extractor) extracts the signal features from several time windows in parallel. The MATLAB code is publicly available and supports several time domain and frequency features

PaSS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0749
application sub category: topic 3168
citation: s12859-019-2901-7
citation: pmcid:PMC6588853
citation: pubmed:31226925
description: Sequencing simulator for PacBio sequencing with a high fidelity.
feature list: operation_0524
feature list: operation 3798
is accessible for free: true
license: GPL-3.0
operating system: Linux
primary contact: Wenmin Zhang

PanGeneHome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3407
citation: arXiv.1805.05597
description: PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. Several standalone tools (e.g. PGAP, PANNOTATOR, PanGP, Roary and BPGA) and web servers (e.g. Panseq, PGAT and PanWeb) dedicated to pangenome analysis have been developed recently and offer the possibility to compute pangenome analysis for genomes provided by a user. For all these tools and servers, users have to collect genomes and manage to run the tools, which implies a significant effort on the user side. To tackle this problem, we developped PanGeneHome, the only web site offering pre-computed pangenome analysis with up-to-date and large scale data. PanGeneHome provides an easy way to get a glimpse on the pangenome of a microbial group of interest, the analysis being precomputed and available for 615 taxa, covering 182 species and 49 orders. Considering the fast growing number of microbial genomes, the PanGeneHome tool will need to be updated regularly.
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

PanTools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic_0102
application sub category: topic_0621
application sub category: topic_0780
application sub category: topic 3174
citation: https://doi.org/10.1101/813634
description: PanTools is a pangenomic toolkit for comparative analysis of large number of genomes. It is developed in the Bioinformatics Group of Wageningen University, the Netherlands.
feature list: operation_0524
feature list: operation 3182
feature list: operation 3198
feature list: operation 3472

Pandoc Scholar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3068
application sub category: topic 3292
application sub category: topic 3315
application sub category: topic 3474
citation: PEERJ.PREPRINTS.2648V2
description: Agilely creating multiple document formats for academic manuscripts with Pandoc Scholar. Create beautiful and semantically meaningful articles with pandoc. science pandoc publishing scientific-writing pandoc-scholar. Plain pandoc is already excellent at document conversion, but it lacks in metadata handling. Pandoc scholar offers simple ways to include metadata on authors, affiliations, contact details, and citations. The data is included into the final output as document headers. Additionally all entries can be exported as JSON-LD, a standardized format for the semantic web. Pandoc a universal document converter. Create beautiful, semantically enriched articles with pandoc. If you need to convert files from one markup format into another, pandoc is your swiss-army knife. (← = conversion from; → = conversion to; ↔︎ = conversion from and to).
feature list: operation_0335
feature list: operation 3431
feature list: operation 3891
license: GPL-2.0
software help: pandoc.org

PanoView
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
citation: JOURNAL.PCBI.1007040
citation: pmcid:PMC6742414
citation: pubmed:31469823
description: An iterative clustering method for single-cell RNA sequencing data | Single-cell Panoramic View Clustering (PanoView) | PanoView is an iterative PCA-based method that integrates with a novel density-based clustering, ordering local maximum by convex hull (OLMC) algorithm, to identify cell subpopulations for single-cell RNA-sequencing. For details of the method, please see our paper at PLOS Computational Biology (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007040)
feature list: operation 2939
feature list: operation 3196
feature list: operation 3891
license: MIT

PanoromiX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3444
citation: s12859-018-2494-6
citation: pmcid:PMC6267067
citation: pubmed:30497372
description: Time-course network medicine platform integrating molecular assays and pathophenotypic data.
feature list: operation_0277
feature list: operation 1781
feature list: operation 3439
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://bioinfo-abcc.ncifcrf.gov/panoromics/#

PaperBot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3068
application sub category: topic 3303
application sub category: topic 3304
citation: s12859-019-2613-z
citation: pmcid:PMC6345070
citation: pubmed:30678631
description: Open-source web-based search and metadata organization of scientific literature.
feature list: operation_0305
feature list: operation 2422
feature list: operation 3431
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: about

ParGenes
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic 3068
citation: bty839
citation: pmcid:PMC6513153
citation: pubmed:30321303
description: Tool for massively parallel model selection and phylogenetic tree inference on thousands of genes.
feature list: operation_0325
feature list: operation_0552
feature list: operation 3478
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: installation
software help: Running-ParGenes
primary contact: Benoit Morel

ParLECH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 3168
citation: S12864-019-6286-9
citation: pmcid:PMC6923905
citation: pubmed:31856721
description: A hybrid and scalable error correction algorithm for indel and substitution errors of long reads. BACKGROUND:Long-read sequencing has shown the promises to overcome the short length limitations of second-generation sequencing by providing more complete assembly. However, the computation of the long sequencing reads is challenged by their higher error rates (e.g., 13% vs. 1%) and higher cost ($0.3 vs. $0.03 per Mbp) compared to the short reads. METHODS:In this paper, we present a new hybrid error correction tool, called ParLECH (Parallel Long-read Error Correction using Hybrid methodology). The error correction algorithm of ParLECH is distributed in nature and efficiently utilizes the k-mer coverage information of high throughput Illumina short-read sequences to rectify the PacBio long-read sequences.
feature list: operation_0524
feature list: operation 3195
feature list: operation 3472

Paragraph
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0625
citation: https://doi.org/10.1101/635011
description: Graph realignment tools for structural variants.
feature list: operation 3196
feature list: operation 3228
feature list: operation 3798
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

Paraload
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Paraload is an original utility which ensures job distribution between thousands of processors, according to the type of the data to be analysed.

PastML
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3293
citation: msz131
citation: pmcid:PMC6735705
citation: pubmed:31127303
description: Fast inference and visualization of ancestral scenarios. PastML infers ancestral characters on a rooted phylogenetic tree with annotated tips, using maximum likelihood or parsimony. The result is then visualised as a zoomable html map.
feature list: operation_0567
feature list: operation 3478
feature list: operation 3745
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: Anna Zhukova
primary contact: Olivier Gascuel

PastView
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic_0610
application sub category: topic 3293
application sub category: topic 3305
citation: https://doi.org/10.1101/651661
description: User-friendly interface to explore evolutionary scenarios.
feature list: operation_0545
feature list: operation 3478
feature list: operation 3745
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Francois Chevenet

Pasteur MLST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Catalogue of public databases for molecular typing and microbial genome diversity.
feature list: operation 3840

PatchSearch
type: SoftwareApplication
input: Protein complex
  type: FormalParameter
  additional type: data 2877
  encoding format: format 1476
input: PDB ID
  type: FormalParameter
  additional type: data 1127
  encoding format: format 1957
output: Match reward score
  type: FormalParameter
  additional type: data 1401
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0166
application sub category: topic 3534
citation: acs.jcim.6b00529
citation: gkz478
citation: pmcid:PMC6602448
citation: pubmed:28282119
citation: pubmed:31131411
description: Identify structurally conserved regions at the protein surfaces.
feature list: operation 3666
is accessible for free: true
license: Freeware
software help: PatchSearch
software version: 1.0
primary contact: Frédéric Guyon
primary contact: Gautier Moroy
primary contact: Julien Rey

Path4Drug
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: fphar.2021.708296
citation: pmcid:PMC8551608
citation: pubmed:34721010
description: The workflow involves a computational technique that employs propagation of drug-protein and protein-protein interactions to predict the biological pathways that are affected by a drug or compound. Reliable, openly available repositories (CHEMBL, TTD, DrugBank, PharmGKB, IUPHAR, Intact, MINT) were used for connecting pharmaceutically relevant compounds to their target proteins in human and the target proteins to their first-degree interactors. Since these databases differ in their architecture and accessibility, diverse sub-workflows with filtering steps were created ensuring the quality of the retrieved data.
feature list: operation 2423

PathBank
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3172
application sub category: topic 3407
citation: gkz861
citation: pmcid:PMC6943071
citation: pubmed:31602464
description: A comprehensive pathway database for model organisms. Quantitative metabolomics services for biomarker discovery and validation. Specializing in ready to use metabolomics kits. Your source for quantitative metabolomics technologies and bioinformatics. PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. A Pathway for Every Protein
feature list: operation_0277
feature list: operation_0533
feature list: operation 3083
feature list: operation 3799

PathCNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
application sub category: topic 3382
application sub category: topic 3474
citation: https://doi.org/10.1101/633123
description: Efficient pan-cancer whole-slide image classification and outlier detection using convolutional neural networks.
feature list: operation 3802
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Readme.md
primary contact: Seda Bilaloglu

PathClass
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 2640
citation: 978-1-4939-9873-9 15
citation: pubmed:31583640
description: De Novo Pathway-Based Classification of Breast Cancer Subtypes. Breast cancer is a heterogeneous disease for which various subtypes have been identified. If you find this web application useful please cite:. Alcaraz et al., De novo pathway-based classification of breast cancer subtypes (manuscript in preparation).
feature list: operation 2495
feature list: operation 3282
feature list: operation 3439

PathFXweb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic 3377
citation: btz419
citation: pmcid:PMC6821302
citation: pubmed:31114840
description: Interaction-network tool to search for the most relevant protein-protein interactions around a drug's target(s), and then analyzes for which phenotypes the network is enriched relative to the entire interaction network.
feature list: operation 3436
feature list: operation 3439
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: about.php

PathFlowAI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
application sub category: topic_0769
application sub category: topic 3474
citation: https://doi.org/10.1101/19003897
description: A High-Throughput Workflow for Preprocessing, Deep Learning and Interpretation in Digital Pathology | A Convenient High-Throughput Workflow for Preprocessing, Deep Learning Analytics and Interpretation in Digital Pathology | MedRxiv Manuscript: https://www.medrxiv.org/content/10.1101/19003897v1 | Fig. 1. PathFlowAI Framework: a) Annotations and whole slide images are preprocessed in parallel using Dask; b) Deep learning prediction model is trained on the model; c) Results are visualized; d) UMAP embeddings provide diagnostics; e) SHAP framework is used to find important regions for the prediction
feature list: operation 3891
license: MIT

PathMe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0091
application sub category: topic_0602
application sub category: topic_0659
citation: s12859-019-2863-9
citation: pmcid:PMC6521546
citation: pubmed:31092193
description: Python package that transforms pathway knowledge from three major pathway databases into a unified abstraction using Biological Expression Language as the pivotal, integrative schema.
feature list: operation_0277
feature list: operation 3083
feature list: operation 3439
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
software help: tutorial
primary contact: Daniel Domingo-Fernández

Pathfinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
citation: F1000RESEARCH.20352.1
description: Open source software for analyzing spatial navigation search strategies | Search Strategy analysis and more for spatial navigation data in rodents | Morris Water Maze search strategy and entropy analysis | For a more detailed overview of Pathfinder please visit our Wiki | Created by Matthew Cooke at The University of British Columbia, Jason Snyder Lab | The Pathfinder package is a search strategy analysis tool for the Morris Water Maze, and can be expanded for other spatial navigation tasks. The program analyses X-Y coordinate data exported from commercially available tracking software. Pathfinder currently supports outputs from: Ethovision, Anymazy, WaterMaze, and ezTrack. We then calculate the best-fit search strategy for the trial. Trials are fit into one of: Direct Swim, Directed Search, Focal Search, Spatial indirect, Chaining, Scanning, Thigmotaxis, and Random Search
license: GPL-3.0

PathwayCommons SPARQL endpoint
type: SoftwareApplication
input: Query script
  type: FormalParameter
  additional type: data 3786
  encoding format: format 3790
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
  encoding format: format 2331
  encoding format: format 2376
  encoding format: format 3261
  encoding format: format 3464
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: SPARQL endpoint
application sub category: topic 2259
application sub category: topic 3307
citation: gkq1039
citation: pmcid:PMC3013659
citation: pubmed:21071392
description: Pathway Commons aims to collect and disseminate biological pathway and interaction data. Data is collected from partner databases and is represented in the BioPAX standard. By representing data in BioPAX, Pathway Commons is able to provide a detailed representation of a variety of biological concepts including: Biochemical reactions; gene regulatory networks; and genetic interactions; transport and catalysis events; and physical interactions involving proteins, DNA, RNA and small molecules and complexes.
feature list: operation_0224
is accessible for free: true
software help: guide
software version: 11
primary contact: https://orcid.org/0000-0003-0185-8861

PathwayCommons web service API
type: SoftwareApplication
input: URI
  type: FormalParameter
  additional type: data 1047
  encoding format: format 2330
input: Identifier
  type: FormalParameter
  additional type: data_0842
  encoding format: format 2330
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 2330
input: Query script
  type: FormalParameter
  additional type: data 3786
  encoding format: format 2330
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
  encoding format: format 3261
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web service
application sub category: topic 2259
application sub category: topic 3307
citation: gkq1039
citation: pmcid:PMC3013659
citation: pubmed:21071392
description: Pathway Commons integrates a number of pathway and molecular interaction databases supporting BioPAX and PSI-MI formats into one large BioPAX model, which can be queried using our web API (documented below). This API can be used by computational biologists to download custom subsets of pathway data for analysis, or can be used to incorporate powerful biological pathway and network information retrieval and query functionality into websites and software.
feature list: operation 2497
is accessible for free: true
software help: swagger-ui.html
software version: 11
primary contact: https://orcid.org/0000-0003-0185-8861

PathwayMatcher
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic_0602
citation: GIZ088
citation: pmcid:PMC6667378
citation: pubmed:31363752
description: Proteoform-centric network construction enables fine-granularity multiomics pathway mapping | PathwayMatcher is a free, open-source software to search for pathways related to a list of genes, proteins or proteoforms in Reactome | PathwayMatcher was benchmarked against different reference datasets covering multiple types of omics data | We present next the Cypher language queries to find the numbers shown in the summary statistics. These can also be used to get the protein-pathway mapping used in PathwayMatcher | PathwayMatcher is a standalone command line tool to match human biomedical data to pathways | PathwayMatcher is a standalone command line tool to match human biomedical data to pathways | 7448 valid tools on Nov 10, 2019
feature list: operation_0277
feature list: operation_0417
feature list: operation_0533
software help: wiki
software help: Performance
software help: queries

Pathways Analyzer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 3407
application sub category: topic 3895
citation: https://doi.org/10.1101/634998
description: Tool for the transformation of metabolic pathways and the development of pathfinding algorithms that establish relevant links between compounds that are essential to the biofuel production process.
feature list: operation 3501
feature list: operation 3660
is accessible for free: true
license: Unlicense
operating system: Linux
software help: README.md

PeCanPIE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3168
citation: GR.250357.119
citation: pmcid:PMC6724669
citation: pubmed:31439692
description: Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE) | St. Jude Children's Research Hospital - Pediatric Cancer Genomic Data Portal | Your web browser (Chrome 68) is out of date. Update your browser for more security, speed and the best experience on this site. Update browser Ignore
feature list: operation 3208
feature list: operation 3225
feature list: operation 3227

PeNGaRoo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3474
application sub category: topic 3510
application sub category: topic 3512
citation: BTZ629
citation: pubmed:31393553
description: Combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. A toolkit for predicting non-classical secreted proteins by combining the gradient boosting machine in an ensemble learning framework . A combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins | In this work, we first constructed a high-quality dataset of experimentally verified “non-classical” secreted proteins, which we then used to create benchmark datasets. Gram-positive bacteria have developed secretion systems to transport proteins across their cell wall, a process that plays an important role during host infection
feature list: operation_0267
feature list: operation_0480

PeSA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3295
citation: https://doi.org/10.1101/760140
description: The Software Tool for Peptide Specificity Analysis (PeSA) is an open-source software designed as a tool to use in the analysis of peptide arrays, permutation arrays and OPALs. The analysis can be used to generate motifs to share the results as a position-specific scoring matrix (PSSM).
feature list: operation_0238
feature list: operation 3631
feature list: operation 3799
license: GPL-3.0

PeakProbe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 3314
application sub category: topic 3474
citation: S2059798319008933
citation: pmcid:PMC6677017
citation: pubmed:31373570
description: Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data | Tool for identifying/classifying solvent molecules in macromolecular x-ray crystal structures | -- Paul Smith, PhD. Assistant Prof. of Chemistry, FordhamUniversity (psmith66@fordham.edu) -- Laurel Jones, PhD Candidate,Northwestern University -- Michael Tynes, Data Sciences GraduateProgram, Fordham University | -- PeakProbe must be run under the "phenix.python" environment or be made aware of the locations of all necessary CCTBX imports -- A PDB file and structure factor data are required and can be specified in any order or suitable format as per PHENIX norms -- The program has several modes of operation and many configurable parameters, but the essentials are covered below
feature list: operation_0417
feature list: operation_0480
feature list: operation 3891

PeanutMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: A mine with peanut data from Legume Information Systems (LIS) PeanutBase
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 0.10

Ped-sim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3318
application sub category: topic 3518
citation: journal.pgen.1007979
citation: pmcid:PMC6944377
citation: pubmed:31860654
description: Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives. Program to simulate pedigree structures. The method can use sex-specific genetic maps and randomly assigns the sex of each parent (or uses user-specified sexes) when using such maps. ./ped-sim -d <in.def> -m -o <out_prefix> --intf <filename>. The above both produce three output files: [out_prefix].seg containing IBD segments, [out_prefix].fam, a PLINK format fam file with all simulated relatives, and [out_prefix].log, a log of what Ped-sim printed to stdout. Sample ids for simulated individuals
feature list: operation_0282
feature list: operation 2944
feature list: operation 3196
feature list: operation 3557
license: GPL-3.0

PedMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3305
application sub category: topic 3322
application sub category: topic 3407
application sub category: topic 3418
citation: S41598-019-54439-W
citation: pmcid:PMC6883068
citation: pubmed:31780760
description: A pediatric diseases map generated from clinical big data from Hangzhou, China. Freelyavailable pediatric critical care data for researchers. Haomin Li#*,Gang Yu#, Cong Dong, Zheng Jia, Jiye An, Huilong Duan, Qiang Shu*. PedMap: a pediatric diseases map generated from clinical big data from Hangzhou, China. Scientfic Report 2019. DOI : 10.1038/s41598-019-54439-w. A pediatric disease map shows the relationships among the most common pediatric diseases, incidence rates, ages of onset and seasonal patterns in children based on more than 5 million outpatient visits at The Children's Hospital Zhejiang University School of Medicine (ZUCH)
feature list: operation 2429
feature list: operation 3432
feature list: operation 3659

PepFoot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: acs.jproteome.9b00238
citation: pubmed:31132275
description: Software package for semi-automated processing of protein footprinting data.
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: UserGuide.pdf
primary contact: Jedd Bellamy-Carter

PepPro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0140
application sub category: topic_0154
application sub category: topic_0820
application sub category: topic 2275
application sub category: topic 3542
citation: jcc.26114
citation: pmcid:PMC7447090
citation: pubmed:31793016
description: PepPro is a Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking.
feature list: operation_0480
feature list: operation_0482
feature list: operation 2488
feature list: operation 3899

PepQuery
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: gr.235028.118
citation: pmcid:PMC6396417
citation: pubmed:30610011
description: Peptide-centric search engine for novel peptide identification and validation.
feature list: operation 3647
feature list: operation 3649
feature list: operation 3755
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: document.html
primary contact: Gitter
primary contact: PepQuery Google Group

PepVis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0769
application sub category: topic 2275
citation: CBDD.13607
citation: pubmed:31441995
description: PepVis tool is a python based GUI pipeline which can be used to model and prepare large-scale peptide structure from the sequence and also to perform large-scale peptide virtual screening. PepVis integrates ModPep and Gromacs for modelling and structure optimization of the peptides, while it integrates AutoDock Vina,ZDOCK, AutoDock CrankPep(ADCP) for performing peptide virtual screening. The protein-peptide complexes can be rescored using ZRANK2 and the flexible refinement of the large protein-peptide complexes can also be performed using FlexPepDock. The parallel job execution has been implemented using GNU parallel and the user can provide inputs using GUI which will produce the bash script based on the customized input provided by the user and can be run in terminal.
feature list: operation_0418
feature list: operation_0482
feature list: operation 3899
license: GPL-3.0

Peptimapper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0121
application sub category: topic 3512
application sub category: topic 3520
citation: s12864-019-5431-9
citation: pmcid:PMC6337836
citation: pubmed:30654742
description: Proteogenomics workflow for the expert annotation of eukaryotic genomes.
feature list: operation 2929
feature list: operation 3643
feature list: operation 3644
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0
primary contact: L. Guillot

PerMemDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0153
application sub category: topic_0621
application sub category: topic_0736
application sub category: topic_0820
application sub category: topic 3068
citation: J.BBAMEM.2019.183076
citation: pubmed:31629694
description: A database for eukaryotic peripheral membrane proteins. The majority of all proteins in cells interact with membranes either permanently or temporarily. Peripheral membrane proteins form transient complexes with membrane proteins and or lipids, via non-covalent interactions and are of outmost importance, due to numerous cellular functions in which they participate. In an effort to collect data regarding this heterogeneous group of proteins we designed and constructed a database, called PerMemDB. PerMemDB is currently the most complete and comprehensive repository of data for eukaryotic peripheral membrane proteins deposited in UniProt or predicted with the use of MBPpred - a computational method that specializes in the detection of proteins that interact non-covalently with membrane lipids, via membrane binding domains. The first version of the database contains 231,770 peripheral membrane proteins from 1009 organisms.
feature list: operation_0224
feature list: operation_0303
feature list: operation 2492
feature list: operation 3431
software help: manual

Pergola-web
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0625
citation: GKZ414
citation: pmcid:PMC6602478
citation: pubmed:31106365
description: Web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards.
feature list: operation_0335
feature list: operation_0337
feature list: operation 3359
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: Cedric Notredame
primary contact: Julia Ponomarenko

PertInInt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic 2640
citation: https://doi.org/10.1101/733485
description: PertInInt is a tool using an integrative approach uncovers genes with perturbed interactions in cancers. The tool enables rapid uncovering of significantly somatically mutated protein functional regions. The goal of the analytical PertInInt method is to rapidly uncover proteins with significant enrichments of somatic Perturbations In Interaction and other functional sites.
feature list: operation_0420
feature list: operation 1812
feature list: operation 3501

PhISCS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0199
citation: GR.234435.118
citation: pmcid:PMC6836735
citation: pubmed:31628256
description: PhISCS is a tool for sub-perfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data. If bulk sequencing data is used, we expect that mutations originate from diploid regions of the genome. Due to variance in VAF values, we recommend the use of bulk data in cases when sequencing depth is at least 1000x (haploid coverage). As output, PhISCS reports tree of tumor evolution together with a set of eliminated mutations, where eliminated mutations represent mutations violating Infinite Sites Assumption (due to deletion of variant allele or due to recurrent mutation) or mutations affected by copy number aberrations that were missed during the tumor copy number profiling (e.g. gain of non-variant allele).
feature list: operation_0487
feature list: operation 3196
feature list: operation 3233

PhaSePro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0219
application sub category: topic_0659
application sub category: topic_0736
application sub category: topic 2229
application sub category: topic 3512
citation: GKZ848
citation: pubmed:31612960
description: PhaSePro is the comprehensive database of proteins driving liquid-liquid phase separation (LLPS) in living cells. LLPS is a molecular process employed by all living organisms to form membraneless organelles, mediating crucial cellular functions. PhaSePro is manually curated, it is solely based on experimentally verified cases of LLPS, integrating a wide range of information on the biophysical driving forces, biological function and regulation of these molecular systems.
feature list: operation_0361
feature list: operation 2422
feature list: operation 3216
feature list: operation 3454
primary contact: Rita Pancsa

PhaSepDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0077
application sub category: topic_0078
application sub category: topic_0121
application sub category: topic 2229
application sub category: topic 3068
citation: gkz847
citation: pmcid:PMC6943039
citation: pubmed:31584089
description: PhaSepDB is a novel database that provides a collection of phase separation related proteins manually curated from publications and public database. In addition to curated proteins, PhaSepDB also provides the researchers with molecular signatures that may facilitate phase separation related proteins identification for all human proteins.
feature list: operation 2421
feature list: operation 3454
feature list: operation 3767

PhagePromoter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3307
citation: btz580
citation: pubmed:31359029
description: PhagePromoter is a python tool that predicts promoter sequences in phage genomes, using machine learning models.
is accessible for free: true

PhageXpress
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 2830
application sub category: topic 3047
application sub category: topic 3168
application sub category: topic 3957
citation: C9LC00978G
citation: pubmed:31712799
description: PhageXress us a Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing.
feature list: operation_0337
feature list: operation 3436
feature list: operation 3795

PharmOmics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3375
application sub category: topic 3377
application sub category: topic 3379
citation: https://doi.org/10.1101/837773
description: PharmOmics is a A Species- and Tissue-specific Drug Signature Database and Online Tool for Toxicity Prediction and Drug Repurposing. It is a Web server for Identifying Pathological Pathways, Networks, and Key Regulators via Multidimensional Data Integration. PharmOmics apps were implemented with Rshiny and depend on javascript. In case of failed loading, please check your antivirus setting and whitelist/temporary disable to solve the issue.
feature list: operation_0277
feature list: operation 3223
feature list: operation 3431
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial pharmomics.php

Pharmmaker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic_0632
application sub category: topic 3047
application sub category: topic 3336
citation: PRO.3732
citation: pmcid:PMC6933858
citation: pubmed:31576621
description: Pharmacophore is a tool for modeling and hit identification based on druggability simulations.
feature list: operation_0482
feature list: operation 2476
feature list: operation 3891
software help: pharmmaker

PheGWAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0153
application sub category: topic 2885
application sub category: topic 3298
application sub category: topic 3517
citation: BTZ944
citation: pubmed:31860083
description: PheGWAS is a three-dimensional approach to dynamically visualize GWAS across multiple phenotypes. It does interactive 3D visualization on many variants many phenotypes
feature list: operation_0337

PheValuator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 3422
citation: j.jbi.2019.103258
citation: j.jbi.2022.104177
citation: pmcid:PMC7736922
citation: pubmed:31369862
citation: pubmed:35995107
description: PheValuator is a phenotype algorithm evaluator.
feature list: operation 2428
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: PheValuator
software version: 2.0

Phen-Gen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3325
citation: nmeth.3046
citation: pubmed:25086502
description: Combines patients' disease symptoms and sequencing data with prior domain knowledge to identify the causative genes for rare disorders.
feature list: operation_0487
feature list: operation 3196
feature list: operation 3501
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

Phen2Gene
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic_0625
application sub category: topic 3325
application sub category: topic 3512
citation: https://doi.org/10.1101/870527
description: Phen2Gene is a phenotype-driven gene prioritization tool, that takes HPO (Human Phenotype Ontology) IDs as inputs, searches and prioritizes candidate causal disease genes. It is distributed under the MIT License by Wang Genomics Lab. Additionally, we have provided a web server and an associated RESTful API service for running Phen2Gene. Finally, a mobile app for Phen2Gene and several other genetic diagnostic tools from our lab is being tested and will be available soon.
feature list: operation 1812
feature list: operation 2422
feature list: operation 3226
license: MIT

PhenX Toolkit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic 3325
application sub category: topic 3517
citation: gim.2016.199
citation: pmcid:PMC5507752
citation: pubmed:28079902
description: Web catalog of high-priority measures for consideration and inclusion in biomedical and epidemiologic research.
feature list: operation 1812
feature list: operation 3196
feature list: operation 3799
is accessible for free: true
license: CC-BY-NC-4.0
operating system: Linux
operating system: Mac
operating system: Windows

PhenoCam
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0610
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3382
application sub category: topic 3810
citation: S41597-019-0229-9
citation: pmcid:PMC6805894
citation: pubmed:31641140
description: PheonoCam is tracking vegetation phenology across diverse biomes using Version 2.0 of the PhenoCam Dataset. This tool facilitates the retrieval and post-processing of PhenoCam time series. The post-processing of PhenoCam data includes outlier removal and the generation of data products such as phenological transition dates.
feature list: operation_0337
feature list: operation 2422
feature list: operation 3435
license: AGPL-3.0
software help: PhenoCam V2.html

PhenoDis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3325
application sub category: topic 3335
application sub category: topic 3577
citation: s13023-018-0765-y
citation: pmcid:PMC5785853
citation: pubmed:29370821
description: Database for phenotypic characterization of rare cardiac diseases.
feature list: operation 2422
feature list: operation 3196
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: showHelp
primary contact: Dr. Andreas Ruepp

PhenoForecaster
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0610
application sub category: topic_0780
application sub category: topic 3810
citation: aps3.1230
citation: pmcid:PMC6426163
citation: pubmed:30937222
description: Software package for the prediction of flowering phenology.
feature list: operation 3659
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Isaac W Park

PhenoGMM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0625
application sub category: topic 3050
application sub category: topic 3697
citation: https://doi.org/10.1101/641464
description: Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity.
feature list: operation 3431
feature list: operation 3557
feature list: operation 3798
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

PhenoGeneRanker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic 3517
citation: https://doi.org/10.1101/651000
description: Gene/disease prioritization tool that utilizes heterogeneous gene disease network.
feature list: operation 3463
feature list: operation 3501
feature list: operation 3766
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

PhenoMeNal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0593
application sub category: topic 3172
application sub category: topic 3298
citation: giy149
citation: pmcid:PMC6377398
citation: pubmed:30535405
description: PhenoMeNal (Phenome and Metabolome aNalysis) is a comprehensive and standardised e-infrastructure that supports the data processing and analysis pipelines for molecular phenotype data generated by metabolomics applications.
feature list: operation 3431
feature list: operation 3435
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Phenomenal-Terms-of-Use-version-11.pdf
software help: wiki

PhenoModifier
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0621
application sub category: topic_0625
application sub category: topic 3295
application sub category: topic 3574
citation: gkz930
citation: pmcid:PMC7145690
citation: pubmed:31642469
description: PhenoModifier is a genetic modifier database for elucidating the genetic basis of human phenotypic variation.
feature list: operation 3196
feature list: operation 3225
feature list: operation 3799

PhenoScanner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Database portal
additional type: Web API
additional type: Web application
application sub category: topic_0102
application sub category: topic 3295
application sub category: topic 3298
citation: btz469
citation: pmcid:PMC6853652
citation: pubmed:31233103
description: Database of human genotype-phenotype associations.
feature list: operation_0487
feature list: operation_0488
feature list: operation 3232
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: information
software version: 2

PhenomeXcan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3298
application sub category: topic 3308
application sub category: topic 3337
application sub category: topic 3517
citation: https://doi.org/10.1101/833210
description: PhenomeXcan is a tool for mapping the genome to the phenome through the transcriptome.
feature list: operation 2429
license: MIT

Phenopolis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic 3325
citation: btx147
citation: pubmed:28334266
description: Open platform for harmonization and analysis of genetic and phenotypic data.
feature list: operation 3226
feature list: operation 3501
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: phenopolis

Phenoscape
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic 2275
application sub category: topic 3067
citation: syz067
citation: pmcid:PMC7672696
citation: pubmed:31596473
description: Phenoscape is a Logical Model of Homology for Comparative Biology.
feature list: operation_0310
feature list: operation_0477
feature list: operation 2421
license: MIT
software help: phenoscape homology.owl

PhiMRF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic_0621
application sub category: topic_0749
application sub category: topic 3170
citation: https://doi.org/10.1101/2019.12.16.878371
description: PhiMRF is an R package for Poisson Hierarchical Markov Random Field model for analysis of spatial dependency on count data.
feature list: operation 3223
feature list: operation 3463
feature list: operation 3800
license: GPL-2.0

PhilDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3077
application sub category: topic 3489
citation: PEERJ.PREPRINTS.1488V2
description: PhilDB is capable of storing data at any frequency supported by Pandas. At this time only daily data has been extensively tested with some limited sub-daily usage. Timeseries database project is for storing potentially changing timeseries data. For example, hydrological data, like streamflow data, where the timeseries may be revised as quality control processes improve the recorded dataset over time.
feature list: operation 2422
software help: module-phildb.database

Phobos
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3068
application sub category: topic 3382
application sub category: topic 3500
citation: FNBEH.2019.00205
citation: pmcid:PMC6753174
citation: pubmed:31572139
description: Phobos is a software for the automated analysis of freezing behavior in rodents. Unlike other programs, it uses manual quantification of a short video to calibrate parameters for optimal freezing detection. Phobos works with 3 user interfaces (UIs) for this purpose. The main user UI is where the user loads videos for quantification, defines an output folder and creates the .xls file with the results. The Video Parameters UI is where the user defines the beginning and end times for freezing detection in the videos and crops the image to restrict the analysis to a specific area. Finally, the Manual Quantification UI is used to manually quantify freezing in a video, which will then be used as a reference for the calibration process.
feature list: operation 2428
feature list: operation 3659
feature list: operation 3799
license: BSD-3-Clause

Phoenix Enhancer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3473
application sub category: topic 3520
citation: https://doi.org/10.1101/846303
description: Phoenix Enhancer is an online service/tool for proteomics data mining using clustered spectra.
feature list: operation 3432
feature list: operation 3631
feature list: operation 3767

Phosphoproteome Prediction
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic 2640
application sub category: topic 3474
citation: btz639
citation: pmcid:PMC7868059
citation: pubmed:31410451
description: Phosphoproteome prediction is a tool for predicting phosphorylation levels of the proteome across cancer patients. It integrates four components into itsalgorithm, including (i) baseline correlations between protein and phosphoprotein abundances, (ii) universal protein–protein interactions, (iii) shareable regulatory information across cancer tissues and (iv) associations among multi-phosphorylation sites of the same protein.
feature list: operation_0417
feature list: operation 2492
feature list: operation 3639

PhyChro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0194
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic 3293
citation: https://doi.org/10.1101/840942
description: PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances.
feature list: operation_0546
feature list: operation 3359
feature list: operation 3478
feature list: operation 3745
license: BSD-3-Clause

PhyDL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0194
application sub category: topic 3293
application sub category: topic 3474
application sub category: topic 3512
citation: https://doi.org/10.1101/787168
description: PhyDL (Phylogenetics by Deep Learning) is a deep learning predictor for phylogenetic reconstruction.
feature list: operation_0323
feature list: operation_0325
feature list: operation_0326
feature list: operation_0551
feature list: operation_0567

SMS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0091
application sub category: topic 2269
application sub category: topic 3293
citation: msx149
citation: pmcid:PMC5850602
citation: pubmed:28472384
description: Phylogenetic model selection using likelihood-based criteria. SMS stends for Smart Model Selection.
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: sms-HowItWorks.pdf
software version: 1.8.4

PhySigs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic 3676
citation: pubmed:31797599
description: PhySigs uses the input of a phylogeny with nodes representing clones in a patient tumor, a signature matrix containing the set of mutational signatures to use in the analysis, and a feature matrix for the set of mutations introduced in each clone. In particular, the mutational categories in the feature matrix should correspond to the mutational categories used in the signature matrix. PhySigs automatically computes the count matrix, as it is simply a diagonal matrix containing the sum of columns in the feature matrix. PhySigs then solves the Tree-constrained Exposure (TE) problem for all possible clusterings of the clones that correspond to a partition of the phylogeny. The output of the TE problem is a relative exposure matrix composed of groups of identical columns corresponding to clusters of clones with identical exposures (denoted by blue and yellow). Edges between these clusters in the phylogeny are interpreted to be where exposure shifts occurred (denoted by a lightning bolt).
feature list: operation_0323
feature list: operation 3435

PhySpeTree
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0194
application sub category: topic_0621
application sub category: topic_0659
application sub category: topic_0769
application sub category: topic 3293
citation: S12862-019-1541-X
citation: pmcid:PMC6889546
citation: pubmed:31791235
description: PhySpeTree is an automated pipeline for reconstructing phylogenetic species trees.
feature list: operation_0325
feature list: operation_0326
feature list: operation_0327
feature list: operation_0544
feature list: operation 3478

Phydelity
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic 3305
application sub category: topic 3324
citation: VEZ039
citation: pmcid:PMC6785678
citation: pubmed:31616568
description: Phydelity, a redesign of PhyCLIP, is a statistically-principled and phylogeny-informed tool capable of identifying putative transmission clusters in pathogen phylogenies without the introduction of arbitrary distance thresholds
feature list: operation_0323
feature list: operation_0326
feature list: operation 3196
feature list: operation 3432
license: LGPL-3.0

Phyllosticta citricarpa
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0780
application sub category: topic 3305
citation: mpp.12861
citation: pmcid:PMC6859488
citation: pubmed:31512371
description: This tool is a gene database for Phyllosticta citricarpa and sister species.
feature list: operation 3216

PhyloCSF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3293
application sub category: topic 3512
application sub category: topic 3517
citation: gr.246462.118
citation: pmcid:PMC6886504
citation: pubmed:31537640
description: PhyloCSF is a method to determine whether a multi-species nucleotide sequence alignment is likely to represent a protein-coding region. PhyloCSF does not rely on homology to known protein sequences; instead, it examines evolutionary signatures characteristic to alignments of conserved coding regions, such as the high frequencies of synonymous codon substitutions and conservative amino acid substitutions, and the low frequencies of other missense and non-sense substitutions (CSF = Codon Substitution Frequencies). One of PhyloCSF’s main current applications is to help distinguish protein-coding and non-coding RNAs represented among novel transcript models obtained from high-throughput transcriptome sequencing.
feature list: operation_0436
feature list: operation 3192
feature list: operation 3216
license: AGPL-3.0

PhyloMagnet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3293
application sub category: topic 3308
application sub category: topic 3837
citation: btz799
citation: pmcid:PMC7703773
citation: pubmed:31647547
description: PhyloMagnet provides fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics. The tool has a pipeline for screening metagenomes, looking for arbitrary lineages, using gene-centric assembly methods and phylogenetics
feature list: operation_0523
feature list: operation_0524
feature list: operation 3258
feature list: operation 3460
feature list: operation 3478
license: GPL-3.0
software help: phylomagnet.readthedocs.io

PhyloNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0194
application sub category: topic_0602
application sub category: topic 3293
citation: BTZ359
citation: pmcid:PMC6612858
citation: pubmed:31510688
description: PhyloNet is a tool that applies a divide-and-conquer method for scalable phylogenetic network inference from multilocus data.
feature list: operation_0547
feature list: operation 3501
feature list: operation 3562

PhyloToL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0194
application sub category: topic 3500
citation: MSZ103
citation: pmcid:PMC6657734
citation: pubmed:31062861
description: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes.
feature list: operation 3478
feature list: operation 3501
feature list: operation 3798
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: manual phyloToL.pdf
primary contact: L. A. Katz
primary contact: Mario Cerón-Romero

PhyreRisk
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0121
application sub category: topic 3120
citation: J.JMB.2019.04.043
citation: pmcid:PMC6597944
citation: pubmed:31075275
description: Dynamic web application that enables the exploration and mapping of genetic variants onto experimental and predicted structures of proteins and protein complexes.
feature list: operation_0302
feature list: operation_0331
feature list: operation 3227
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: http://phyrerisk.bc.ic.ac.uk/
software help: faq
primary contact: Alessia David

PhysMPrePro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0081
application sub category: topic_0749
application sub category: topic 3318
application sub category: topic 3512
citation: J.YGENO.2019.12.001
citation: pubmed:31809797
description: PhysMPrePro is an energy model for recognizing the prokaryotic promoters based on molecular structure.
feature list: operation_0372
feature list: operation_0440

PhysiCell
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 2259
application sub category: topic 3316
citation: c9me00036d
citation: journal.pcbi.1005991
citation: pmcid:PMC5841829
citation: pmcid:PMC6690424
citation: pubmed:29474446
citation: pubmed:31497314
description: PhysiCell is a physics-based cell simulator.
feature list: operation 2476
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: physicell-tutorials

PhytoMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: An InterMine interface to data from Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, which hosts 81 assembled and annotation genomes, from 78 viridiplantae species.
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 13 (phytomine-13.0)

PhytoTypeDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0121
application sub category: topic_0780
application sub category: topic 3168
citation: bay125
citation: pmcid:PMC6301341
citation: pubmed:30576486
description: Database of plant protein inter-cultivar variability and function.
feature list: operation_0267
feature list: operation 2422
feature list: operation 3196
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: about

PiMP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3520
citation: btx499
citation: pmcid:PMC5860087
citation: pubmed:28961954
description: PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data.
feature list: operation 3803
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: userguide
primary contact: Karl Burgess

PiPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0736
application sub category: topic 3542
citation: S41598-019-43189-4
citation: pmcid:PMC6499831
citation: pubmed:31053765
description: Deep-learning method for prediction of π-helices in protein sequences.
feature list: operation_0468
feature list: operation_0469
feature list: operation_0470
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Stanislaw Dunin-Horkawicz

PiVR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic 3068
application sub category: topic 3304
application sub category: topic 3500
citation: journal.pbio.3000712
description: PiVR is a closed-loop platform to study unrestrained sensorimotor behavior. PiVR has been developed to track a variety of animals in real time and present them with light stimuli.
feature list: operation 3431
feature list: operation 3435
software help: latest

PicturedRocks
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2229
application sub category: topic 3390
application sub category: topic 3512
citation: https://doi.org/10.1101/646919
description: Single Cell RNA-seq Analysis Tool.
feature list: operation 3798
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest
primary contact: Umang Varma

PinMol
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0632
application sub category: topic 3382
application sub category: topic 3512
citation: rna.069542.118
citation: pmcid:PMC6380279
citation: pubmed:30573696
description: Application for designing molecular beacons for live cell imaging of endogenous mRNAs.
feature list: operation_0278
feature list: operation_0279
feature list: operation_0502
is accessible for free: true
license: GPL-3.0
operating system: Mac
operating system: Windows
software help: tutorial-pinmol-mac
software version: beta 1.0
primary contact: Irina E. Catrina

PingPongPro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0659
application sub category: topic_0798
application sub category: topic 3512
citation: bty578
citation: pubmed:29985981
description: Tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data.
feature list: operation_0427
feature list: operation 2495
feature list: operation 3227
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Sebastian Uhrig

PipeMEM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0654
application sub category: topic_0769
application sub category: topic 3168
citation: GENES10110886
citation: pmcid:PMC6896194
citation: pubmed:31689965
description: PipeMEM is a Framework to Speed Up BWA-MEM in Spark with Low Overhead.
feature list: operation 3096
feature list: operation 3182
feature list: operation 3802

PlaNET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2885
application sub category: topic 3295
application sub category: topic 3518
citation: https://doi.org/10.1101/618470
description: R package for inferring ethnicity from placental DNA methylation microarray data.
feature list: operation_0417
feature list: operation 3196
feature list: operation 3891
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Victor Yuan

PlaSMo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 2259
application sub category: topic 3489
citation: WELLCOMEOPENRES.15341.2
citation: pmcid:PMC6652102
citation: pubmed:31363499
description: PlaSMo stands for Plant Systems-biology Modelling and the mission of the project was ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.
feature list: operation_0481
feature list: operation 2422
feature list: operation 3431
license: MIT

PlaScope
type: SoftwareApplication
input: Sequence assembly
  type: FormalParameter
  additional type: data_0925
  encoding format: format 1929
input: Sequence trace
  type: FormalParameter
  additional type: data_0924
  encoding format: format 1931
output: Sequence profile
  type: FormalParameter
  additional type: data 1354
  encoding format: format 2069
output: Sequence profile
  type: FormalParameter
  additional type: data 1354
  encoding format: format 2069
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0621
application sub category: topic_0798
author: https://orcid.org/0000-0001-9092-8336
citation: mgen.0.000211
citation: pmcid:PMC6202455
citation: pubmed:30265232
contributor: Mathieu Dubois
description: PlaScope is a targeted approach to assess the plasmidome of bacteria.
feature list: operation_0525
feature list: operation 2995
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
software version: 1.3.1
primary contact: https://orcid.org/0000-0001-9092-8336

PlanExp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3512
citation: BTZ802
citation: pubmed:31647529
description: PlanExp is an intuitive integration of complex RNA-seq datasets with planarian omics resources.
feature list: operation_0571
feature list: operation 2940
feature list: operation 3223
feature list: operation 3439

PlanMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: An integrated web resource of data & tools to mine Planarian biology
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 3.0

Plant
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic_0780
application sub category: topic 3512
citation: https://doi.org/10.1101/756858
description: Plant is a website and database provides systematic annotations of all types of endogenous plant small RNA loci.
feature list: operation 3216
feature list: operation 3792

PlantAPAdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0621
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3512
citation: PP.19.00943
citation: pubmed:31767692
description: PlantAPAdb provides a comprehensive and manually curated catalog of APA sites in plants based on a large volume of data from diverse biological samples generated by 3′ seq. Currently, PlantAPAdb contains APA sites in seven plant organisms, including Oryza sativa L. (japonica and indica), Arabidopsis thaliana, Chlamydomonas reinhardtii, Medicago truncatula, Trifolium pratense, Populus trichocarpa and Phyllostachys edulis.
feature list: operation_0428
feature list: operation 2421
feature list: operation 2422

PlantAligDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0637
application sub category: topic_0780
application sub category: topic 3810
citation: https://doi.org/10.1101/617035
description: Web-based platform of nucleotide sequence alignments of plants.
feature list: operation_0499
feature list: operation 3200
feature list: operation 3460
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: PlantAligDB description.html
primary contact: Filipe Pereira

PlantCircNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic_0780
application sub category: topic 3512
citation: BAX089
citation: pmcid:PMC5727401
citation: pubmed:31725858
description: PlantCircNet is a database that provides plant circRNA-miRNA-gene regulatory networks, as well as circRNA information and circRNA expression profiles. It provides convenient search functions for circRNA-associated regulatory networks and enables users to retrieve regulatory interactions of interest by circRNAs, miRNAs and mRNAs across eight model species. Sequences search is also available. And an enrichment analysis tool has been provided for Gene Ontology categories of miRNA targets.
feature list: operation_0463
feature list: operation 2421
feature list: operation 3083
feature list: operation 3501
feature list: operation 3792

PlantRegMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0204
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3169
citation: GKZ1020
citation: pubmed:31701126
description: PlantRegMap is a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them, advancing the understanding of plant transcriptional regulatory system.
feature list: operation_0438
feature list: operation 2422
feature list: operation 2429
feature list: operation 2575

PlantSimLab
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0780
application sub category: topic 2259
application sub category: topic 3315
citation: S12859-019-3094-9
citation: pmcid:PMC6805577
citation: pubmed:31638901
description: PlantSimLab is a modeling and simulation web tool for plant biologists.
feature list: operation_0337
feature list: operation 2426
feature list: operation 3891

Plant DataDiscovery
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Keyword
  type: FormalParameter
  additional type: data_0968
output: Database search results
  type: FormalParameter
  additional type: data 2080
output: Data reference
  type: FormalParameter
  additional type: data 2093
output: Identifier
  type: FormalParameter
  additional type: data_0842
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
additional type: Web application
additional type: Web service
application sub category: topic_0091
application sub category: topic_0610
application sub category: topic_0780
application sub category: topic 3071
application sub category: topic 3810
citation: hortres.2016.56
citation: s13059-018-1491-4
description: The purpose of this web portal is to facilitate the discoverability of public data on plant biology managed by different laboratories across the world. The web portal indexes and makes findable any kind of plant data. Plant DataDiscovery is an implementation of DataDiscovery.
feature list: operation_0227
feature list: operation 2421
feature list: operation 3625
feature list: operation 3908
is accessible for free: true
license: BSD-3-Clause
software help: about
software help: help
software help: join
software help: legal
primary contact: Support service

Plant Reactome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic_0780
application sub category: topic 3407
application sub category: topic 3810
citation: gkz996
citation: pmcid:PMC7145600
citation: pubmed:31680153
description: Plant Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of plant pathway knowledge.
feature list: operation_0277
feature list: operation_0533
feature list: operation 2436
feature list: operation 3083

Plant Regulomics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 3173
application sub category: topic 3174
citation: TPJ.14526
citation: pubmed:31494994
description: Plant Regulomics is a data-driven interface for retrieving upstream regulators from plant multi-omics data, which integrates 20,737 transcriptomic and epigenomic data sets and diverse sources of functional evidence (58,112 functional terms and 695,414 protein-protein interactions) from six plant species, namely Arabidopsis thaliana, Oryza sativa, Zea mays, Glycine max, Solanum lycopersicum and Triticum aestivum, along with the orthologous genes from 56 whole-genome sequenced plant species. These data were well-organized to gene modules and further implemented into the same statistical framework.
feature list: operation 2422
feature list: operation 2495
feature list: operation 3501

PlasClass
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0654
application sub category: topic 3174
application sub category: topic 3837
citation: https://doi.org/10.1101/783571
description: PlasClass is a tool for easy classification of sequences as either plasmid or chromosomal. For example, it can be used to classify the contigs in a (metagenomic) assembly.
feature list: operation_0310
feature list: operation 2995
feature list: operation 3472
license: MIT

PlasmidFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0632
application sub category: topic 3673
citation: 978-1-4939-9877-7 20
citation: pubmed:31584170
description: PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).
feature list: operation_0525
feature list: operation 3216
feature list: operation 3840

Plasmodesma
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0593
application sub category: topic_0780
application sub category: topic 3474
citation: C8FD00242H
citation: pubmed:31120045
description: Automatised pharmacophoric deconvolution of plant extracts.
feature list: operation_0337
feature list: operation 3501
feature list: operation 3629
is accessible for free: true
license: CECILL-1.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Marc-André Delsuc

Plass
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 1929
  encoding format: format 1930
output: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3308
author: http://orcid.org/0000-0001-8637-6719
author: http://orcid.org/0000-0001-8781-9753
citation: s41592-019-0437-4
citation: https://doi.org/10.1101/386110
citation: pubmed:31235882
description: Protein-Level ASSembler (PLASS): sensitive and precise protein assembler
feature list: operation_0310
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software version: 1-2e0ef
software version: 2-c7e35
software version: 3-764a3
software version: 4-687d7
primary contact: http://orcid.org/0000-0001-8781-9753
primary contact: http://orcid.org/0000-0001-9642-8244

Plastid Genome Annotator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0780
application sub category: topic 3293
application sub category: topic 3512
citation: s13007-019-0435-7
citation: pmcid:PMC6528300
citation: pubmed:31139240
description: Software package for rapid, accurate, and flexible batch annotation of plastomes.
feature list: operation_0224
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Xiao-Jian Qu

Platon
type: SoftwareApplication
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0798
author: http://orcid.org/0000-0003-4216-2721
citation: mgen.0.000398
citation: pmcid:PMC7660248
citation: pubmed:32579097
description: Identification and characterization of bacterial plasmid contigs from short-read draft assemblies.
feature list: operation 2995
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: platon
software version: 1.6
primary contact: http://orcid.org/0000-0003-4216-2721

PleioNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic_0634
citation: btz179
citation: pmcid:PMC6792104
citation: pubmed:30865284
description: Web-based visualization tool for exploring pleiotropy across complex traits.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: pleionet
primary contact: X. R. Gao

PlotTwist
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3304
application sub category: topic 3382
citation: https://doi.org/10.1101/745612
description: PlotTwist (Plotting data from Time-lapse experiments With Indicators of conditions at Set Times) is an app for visualizing the data and statistics of continuous data, with a focus on time-dependent measurements. The philosophy of the approach is that plotting the raw data (instead of a summary) improves transparency and interpretation. To facilitate the visualization of individual measurements, the data can be shown as 'small mutliples' or in 'heatmap-style'. To further facilitate the comparison, the mean and 95% CI can be added. The user has full control over the visibility of the raw data and statistics by adjustment of the transparency (alpha). Several color blind friendly palettes are available to label the data. The comparison of multiple conditions is enabled by multiple file upload (csv or xls format), where each file represents a condition.
feature list: operation_0337
feature list: operation 1812
feature list: operation 3798

Pluto
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2830
application sub category: topic 3474
application sub category: topic 3500
application sub category: topic 3520
citation: J.YCZZ.19-155
citation: pubmed:31735706
description: MHC-I epitope presentation prediction based on transfer learning.
feature list: operation_0252
feature list: operation_0416

PmiREN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0659
application sub category: topic_0780
application sub category: topic 3293
application sub category: topic 3512
citation: gkz894
citation: pmcid:PMC6943064
citation: pubmed:31602478
description: PmiREN is a comprehensive encyclopedia of plant miRNAs.
feature list: operation_0463
feature list: operation 2422
feature list: operation 3192
feature list: operation 3792

PnGT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0218
application sub category: topic 3474
author: Shubham Vishnoi
citation: CBDD.13617
citation: pubmed:31483930
description: PnGT stand for 'Physicochemical n-Grams Tool'. It is a tool for protein physicochemical descriptor generation . Physicochemical n-Grams Tool (PnGT) is an open source standalone software for calculating physicochemical descriptors of protein developed using the Python scripting language.
feature list: operation 2423
feature list: operation 2426
feature list: operation 2930
software help: tutorial.html

Pneumocystis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic 3174
application sub category: topic 3519
application sub category: topic 3577
application sub category: topic 3837
citation: MYZ109
citation: pubmed:31758176
description: Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens.
feature list: operation_0337
feature list: operation 3200
feature list: operation 3431
license: MIT

PointFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0199
application sub category: topic_0654
application sub category: topic 3517
application sub category: topic 3673
citation: FMICB.2019.02464
citation: pmcid:PMC6834686
citation: pubmed:31736907
description: PointFinder is an Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites.
feature list: operation 3202
feature list: operation 3482
feature list: operation 3695

PointSite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0166
application sub category: topic_0209
application sub category: topic 3534
citation: https://doi.org/10.1101/831131
description: PointSite is a point cloud segmentation tool for identification of protein ligand binding atoms.
feature list: operation_0482
feature list: operation 2575
feature list: operation 3767

PolyASite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3308
application sub category: topic 3512
citation: gkz918
citation: pmcid:PMC7145510
citation: pubmed:31617559
description: PolyASite is a consolidated atlas of polyadenylation sites from 3' end sequencing. A portal to the curated set of poly(A) sites that we inferred in the human, mouse and worm genomes, based on all 3’ end sequencing datasets that we could identify in the SRA nucleotide database as of June 2019.
feature list: operation_0363
feature list: operation_0428
feature list: operation 3208

PPB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3336
application sub category: topic 3377
citation: s13321-017-0199-x
citation: pmcid:PMC5319934
citation: pubmed:28270862
description: PolyPharmacology Browser (PPB) - Web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data
feature list: operation 2489
feature list: operation 2929
feature list: operation 3501
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Mahendra Awale
primary contact: Prof. Jean Louis Reymond

PolySTest
type: SoftwareApplication
input: Expression data
  type: FormalParameter
  additional type: data 2603
  encoding format: format 3751
  encoding format: format 3752
output: Heat map
  type: FormalParameter
  additional type: data 1636
  encoding format: format 3604
output: Q-value
  type: FormalParameter
  additional type: data 3932
  encoding format: format 3752
output: Histogram
  type: FormalParameter
  additional type: data 3905
  encoding format: format 3604
output: Gene expression profile
  type: FormalParameter
  additional type: data_0928
  encoding format: format 3752
output: P-value
  type: FormalParameter
  additional type: data 1669
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic 2269
application sub category: topic 3520
citation: mcp.RA119.001777
citation: pmcid:PMC8015005
citation: pubmed:32424025
description: Robust statistical testing of quantitative proteomics data. The tool comprises and combines different tests and includes a new method for combined statistics of quantitative and missing values.
feature list: operation 3664
feature list: operation 3741
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac

PopDel
type: SoftwareApplication
input: Sequence alignment (nucleic acid)
  type: FormalParameter
  additional type: data 1383
  encoding format: format 2572
output: Sequence variations
  type: FormalParameter
  additional type: data 3498
  encoding format: format 3016
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3175
application sub category: topic 3325
author: Sebastian Roskosch
description: A tool for population level deletion calling from short paired-end sequence reads.
feature list: operation 3196
feature list: operation 3227
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
software version: 1.1.1
primary contact: https://orcid.org/0000-0002-3417-7504

PopInf
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic 2640
citation: https://doi.org/10.1101/823344
description: An approach for reproducibly visualizing and assigning population affiliation in genomic samples of uncertain origin. Quick inference of population history. PopInf is a method to infer the major population (or populations) ancestry of a sample or set of samples. Below are steps for running PopInf. PopInf is incorporated into the workflow system snakemake. All necessary files and scripts are in this directory. There are instructions on preparing the reference panel in a folder called "Reference_Panel". There are also instructions on preparing the unknown samples in a folder called "Unknown_Samples"
feature list: operation 2939
feature list: operation 3196
feature list: operation 3891

PopLDdecay
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3168
citation: bty875
citation: pubmed:30321304
description: Tool for linkage disequilibrium decay analysis based on variant call format files.
feature list: operation_0488
feature list: operation 3196
feature list: operation 3227
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: Manual.pdf
software help: README.md
primary contact: Wei-Ming He

PopNetD3
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2885
application sub category: topic 3796
application sub category: topic 3810
citation: evz100
citation: pmcid:PMC6668580
citation: pubmed:31095319
description: Network-Based Web Resource for Exploring Population Structure.
feature list: operation_0337
feature list: operation 3196
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: popnetd3
primary contact: John Parkinson

PopTargs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0160
application sub category: topic_0659
application sub category: topic 2885
application sub category: topic 3056
application sub category: topic 3170
citation: BAZ102
citation: pmcid:PMC6790967
citation: pubmed:31608947
description: PopTargs is a database for studying population evolutionary genetics of human microRNA target sites. These are the scripts used to create the MySQL database that is used by PopTargs.essex.ac.uk. The pipeline can be altered to create similar databases with different species, it may need to be adjusted to fit your file names.
feature list: operation_0337
feature list: operation_0463
feature list: operation 2421
license: MIT

Portal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 2885
application sub category: topic 3305
application sub category: topic 3517
citation: mds.27873
citation: pmcid:PMC6973052
citation: pubmed:31659794
description: The Parkinson's Disease Mendelian Randomization Research Portal. iPDGC PD MR Research Portal
feature list: operation_0484
feature list: operation 3196
feature list: operation 3659

Porter
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic 3542
citation: 978-3-030-02634-9 10
citation: s41598-019-48786-x
citation: pmcid:PMC6710256
citation: pubmed:31451723
description: Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes
feature list: operation_0267
feature list: operation_0468
feature list: operation_0469
feature list: operation_0470
is accessible for free: true
license: CC-BY-NC-SA-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: quickhelp.html
software version: 5

Porter5
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0078
application sub category: topic 2814
application sub category: topic 3542
citation: 978-3-030-02634-9 10
citation: s41598-019-48786-x
citation: https://doi.org/10.1101/289033
citation: pmcid:PMC6710256
citation: pubmed:31451723
description: Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes
feature list: operation_0267
feature list: operation_0468
feature list: operation_0469
feature list: operation_0470
is accessible for free: true
license: CC-BY-NC-SA-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: quickhelp.html
software version: 5

Potpourri
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic_0749
application sub category: topic 2885
application sub category: topic 3517
application sub category: topic 3676
citation: cmb.2020.0429
citation: https://doi.org/10.1101/830216
citation: pubmed:33275856
description: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection. Potpourri provides a MATLAB interface for ease of use. These instructions will guide you to build and run Potpourri on MATLAB.
feature list: operation_0484
feature list: operation 2238
feature list: operation 3196
license: GPL-3.0

PowerShell
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: 978-1-4939-9744-2 17
citation: pubmed:31552639
description: Using the Object-Oriented PowerShell for Simple Proteomics Data Analysis | Scripting languages such as Python and Bash are appreciated for solving simple, everyday tasks in bioinformatics
feature list: operation_0335
feature list: operation 1812
feature list: operation 3631

PrAnCER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0611
application sub category: topic 3304
application sub category: topic 3401
citation: https://doi.org/10.3791/59596
citation: pmcid:PMC6827337
citation: pubmed:31449248
description: A Low-Cost, Open-Access Automated Gait Analysis System for Assessing Motor Deficits | Gait analysis is used to quantify changes in motor function in many rodent models of disease. Despite the importance of assessing gait and motor function in many areas of research, the available commercial options have several limitations such as high cost and lack of accessible, open code. To address these issues, we developed PrAnCER, Paw-Print Analysis of Contrast-Enhanced Recordings, for automated quantification of gait. The contrast-enhanced recordings are produced by using a translucent floor that obscures objects not in contact with the surface, effectively isolating the rat's paw prints as it walks. Using these videos, our simple software program reliably measures a variety of spatiotemporal gait parameters. To demonstrate that PrAnCER can accurately detect changes in motor function, we employed a haloperidol model of Parkinson's disease (PD)
feature list: operation 3799

PrankWeb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic 3474
application sub category: topic 3534
citation: gkz424
citation: s13321-018-0285-8
citation: pmcid:PMC6091426
citation: pmcid:PMC6602436
citation: pubmed:30109435
citation: pubmed:31114880
description: Web application for protein-ligand binding sites analysis and visualization | This repositary contains PrankWeb web application.
feature list: operation 2575
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: https://orcid.org/0000-0003-4679-0557

PreSNO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic_0749
application sub category: topic 3474
citation: C9MO00098D
citation: pubmed:31710075
description: Prediction of S-nitrosylation sites by integrating support vector machines and random forest. PreSNO is only available to academic users
feature list: operation_0417

PreciseDose
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: The PreciseDose system represents the first integrated computational environment combining classical pharmacokinetic–pharmacodynamic modeling with quantum-biological digital twin simulation. It enables organ-level prediction of drug absorption and distribution through AI-assisted algorithms and real-time numerical solvers. The system has been validated using external pharmacokinetic datasets and benchmarked against established models (Teoreler data). Outputs include physiologically accurate dose simulations and interactive 3D distribution maps. This record introduces a novel multidisciplinary advancement in precision pharmacology and computational medicine.

Pred-BVP-Unb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3912
citation: j.ygeno.2019.09.006
citation: pubmed:31526842
description: Fast prediction of bacteriophage Virion proteins using un-biased multi-perspective properties with recursive feature elimination | Bacteriophage virion proteins (BVPs) are bacterial viruses that have a great impact on different biological functions of bacteria. They are significantly used in genetic engineering and phage therapy applications. Correct identification of BVP through conventional pathogen methods are slow and expensive. Thus, designing a Bioinformatics predictor is urgently desirable to accelerate correct identification of BVPs within a huge volume of proteins. However, available prediction tools performance is inadequate due to the lack of useful feature representation and severe imbalance issue. In the present study, we propose an intelligent model, called Pred-BVP-Unb for discrimination of BVPs that employed three nominal sequences-driven descriptors, i.e

Pred-MutHTP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0199
application sub category: topic_0736
application sub category: topic_0820
application sub category: topic 3474
citation: HUMU.23961
citation: pubmed:31821684
description: Prediction of disease-causing and neutral mutations in human transmembrane proteins. Transmembrane proteins (TMPs) act as a gate to the interior of the cells. A tool to discriminate the disease-causing and neutral mutations of membrane proteins. We have used 4 different type of datasets for developing the classification models and these datasets are available in the follwoing link
feature list: operation_0269
feature list: operation_0331
feature list: operation 2241

PredPRBA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic 2275
citation: FGENE.2019.00637
citation: pmcid:PMC6688581
citation: pubmed:31428122
description: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees | Prediction of protein-RNA binding affinity | PredPRBA, a computational method that can effectively predict Protein-RNA Binding Affinity using Machine Learning Algorithm
feature list: operation 3659
feature list: operation 3901
feature list: operation 3902

PredPSI-SVR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic 3320
application sub category: topic 3512
citation: humu.23785
citation: pmcid:PMC6744342
citation: pubmed:31070294
description: Predicting the change of percent spliced in (delta-PSI or ) caused by genetic variants.
feature list: operation_0433
feature list: operation_0446
feature list: operation 3659
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: README.md
primary contact: Huiying Zhao
primary contact: Yuedong Yang

PrimerMiner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0632
application sub category: topic 3050
application sub category: topic 3168
application sub category: topic 3500
citation: PEERJ.PREPRINTS.2044V2
description: PrimerMiner is an R package for the development and validation of DNA metabarcoding COI primers for aquatic invertebrates.
feature list: operation_0308
feature list: operation 3192
feature list: operation 3200
feature list: operation 3237

PriorCD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3336
application sub category: topic 3375
application sub category: topic 3379
citation: https://doi.org/10.1002/1878-0261.12564
citation: pmcid:PMC6763777
citation: pubmed:31408580
description: Prioritization of candidate cancer drugs based on a drug functional similarity network constructed by integrating pathway activities and drug activities | Prioritizing Cancer Drugs for Interested Cancer | Prioritize candidate cancer drugs for drug repositioning based on the random walk with restart algorithm in a drug-drug functional similarity network. 1) We firstly constructed a drug-drug functional similarity network by integrating pathway activity and drug activity derived from the NCI-60 cancer cell lines. 2) Secondly, we calculated drug repurposing score according to a set of approved therapeutic drugs of interested cancer based on the random walk with restart algorithm in the drug-drug functional similarity network. 3) Finally, the permutation test was used to calculate the statistical significance level for the drug repurposing score
feature list: operation 2436
feature list: operation 3223
license: GPL-2.0

ProAffiMuSeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic_0199
citation: BTZ829
citation: pubmed:31713585
description: Sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification. This server predicts protein-protein binding affinity change upon mutation using sequence-based features and functional class. ProAffiMuSeq shows a correlation of 0.73 and a mean absolute error (MAE) of 0.86 kcal/mol in cross-validation. In the test dataset, the performance remains consistent with a correlation of 0.75 with MAE of 0.94 kcal/mol. In a blind dataset of 473 mutations (Geng et al. 2019, Proteins 87, 110-119) it showed a correlation and MAE of 0.27 and 1.06 kcal/mol, respectively, comparable to structure-based methods. Further, our method showed a MAE of 1.21 kcal/mol, when tested with a set of 552 additional non-redundant interface mutations in 80 complexes deposited in SKEMPI 2.0 (Jankauskaitė et al. 2019, Bioinformatics 35, 462-469)
feature list: operation 2464
feature list: operation 2492
feature list: operation 3431

ProCarbDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0078
application sub category: topic_0152
application sub category: topic_0154
application sub category: topic_0199
citation: gkz860
citation: pmcid:PMC6943041
citation: pubmed:31598690
description: a database of carbohydrate-binding proteins. An open access database ready to answer your sweetest queries. Carbohydrate-binding proteins play crucial roles across all viruses and organisms
feature list: operation_0224
feature list: operation_0570
feature list: operation 3092

ProGeo-neo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2830
citation: https://doi.org/10.1101/719351
description: a Customized Proteogenomic Workflow for Neoantigen Prediction and Selection | ProGeo-neo requires a Linux operation system (centos6) with Python (V2.7) , Perl and Java installed
feature list: operation_0252
feature list: operation 3211

ProPheno
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic_0625
application sub category: topic 2640
application sub category: topic 3325
citation: PEERJ.PREPRINTS.27479V2
description: An online dataset for accelerating the complete characterization of the human protein-phenotype landscape in biomedical literature. Identifying protein-phenotype relations is of paramount importance for applications such as uncovering rare and complex diseases. One of the best resources that captures the protein-phenotype relationships is the biomedical literature. In this work, we introduce ProPheno, a comprehensive online dataset composed of human protein phenotype mentions extracted from the complete corpora of Medline and PubMed Central Open Access. Moreover, it includes co-occurrences of protein-phenotype pairs within different spans of text such as sentences and paragraphs. We use ProPheno for completely characterizing the human protein-phenotype landscape in biomedical literature
feature list: operation_0306
feature list: operation 3778

ProSNEx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic_0602
citation: GKZ390
citation: pmcid:PMC6602423
citation: pubmed:31114881
description: Web-based application for exploration and analysis of protein structures using network formalism.
feature list: operation_0244
feature list: operation_0272
feature list: operation 2950
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.pdf
primary contact: https://orcid.org/0000-0002-3043-0015
primary contact: Onur Sercinoglu
primary contact: Rasim Murat Aydinkal

ProSampler
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3169
citation: btz290
citation: pmcid:PMC6853706
citation: pubmed:31070745
description: Ultra-fast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery.
feature list: operation_0238
feature list: operation_0239
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Yang Li
primary contact: Zhengchang Su

ProTargetMiner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3336
application sub category: topic 3520
citation: S41467-019-13582-8
citation: pmcid:PMC6915695
citation: pubmed:31844049
description: ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery. Automated online software for anticancer drug target/mechanism deconvolution. . ProTargetMiner is also available directly through this web page: http://protargetminer.genexplain.com. The ProTargetMiner R Shiny package is an automated online software for anticancer drug target mechanism deconvolution
feature list: operation_0337
feature list: operation 3629
feature list: operation 3767

ProTstab
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic 3474
citation: S12864-019-6138-7
citation: pmcid:PMC6830000
citation: pubmed:31684883
description: predictor for cellular protein stability. Tool for classification of protein variations predictor. A benchmark database for variations. Datasets for training and testing cellular protein stability predictor ProTstab:. Stability of biomolecules, especially of proteins, is of great interest and significance. Protein stability has been the major target for protein engineering, mainly to increase the stability, but sometimes also to destabilize proteins . Effects on stability are among the most common consequences for disease-related variations , thus this phenomenon is of interest for variation interpretation to explain the effects of harmful variants. We trained a novel machine learning tool for prediction of protein stability, especially melting temperature Tm. The tool is based on amino acid sequence information and using GBRT (Gradient boosting of regression trees) algorithm.
feature list: operation_0267
feature list: operation_0331
feature list: operation 2489
feature list: operation 3659

ProcMod
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0610
application sub category: topic 3047
citation: https://doi.org/10.1101/842070
description: Assessing the shared variation among high-dimensional data matrices. Réflexions autour de l'analyse de la variance basée sur une analyse type procuste pour estimé la part de la variance d'un tableau expliquée par un ou plusieurs autres tableaux
feature list: operation_0337
feature list: operation 3659
feature list: operation 3891

PromPDD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2830
application sub category: topic 3047
citation: J.JIM.2019.112685
citation: pubmed:31678214
description: web-based tool for the prediction, deciphering and design of promiscuous peptides that bind to HLA class I molecules. PromPDD :HLA peptide-binding fingerprints : HLAsupE : Publication : Download: tutorial. PromPDD were developed based on the prediction models generated using the average relative binding (ARB) matrix method.PromPDD enables the prediction and deciphering of promiscuous peptides that bind to multiple HLA molecules within or cross HLA supertypes in a simpler and more direct way. We expanded the application of PromPDD to HLA class I alleles with limited experimentally verified data by generating pan-specific matrices using a derived modular method, and more than 2500 HLA molecules encoded by HLA-A and -B genes are available in PromPDD
feature list: operation_0252
feature list: operation_0416
feature list: operation 3461

PromoterPredict
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0749
application sub category: topic 3398
application sub category: topic 3474
citation: PEERJ.PREPRINTS.26759V2
description: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence. Machine Learning using Multivariate Linear Regression to Predict the Strength of a Promoter.
feature list: operation_0321
feature list: operation_0440
feature list: operation 3659

Prophage Hunter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3293
application sub category: topic 3474
application sub category: topic 3557
citation: GKZ380
citation: pmcid:PMC6602508
citation: pubmed:31114893
description: Integrative tool that employs similarity matching within our customized phage parts library and machine learning of prophage genetic features, to score the probability of a prophage being active.
feature list: operation_0310
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: Tutorial.html
primary contact: https://orcid.org/0000-0002-0507-7352

Prosit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: s41592-019-0426-7
citation: pubmed:31133760
description: Proteome-wide prediction of peptide tandem mass spectra by deep learning.
feature list: operation 3627
feature list: operation 3649
feature list: operation 3801
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: faq
primary contact: Prof. Dr. Bernhard Küster

Prot-SpaM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0121
application sub category: topic_0194
citation: giy148
citation: pmcid:PMC6436989
citation: pubmed:30535314
description: Alignment-free phylogeny reconstruction based on whole-proteome sequences.
feature list: operation_0289
feature list: operation_0557
feature list: operation 3478
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Jendrik Schellhorn

ProtFus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0218
application sub category: topic 3512
citation: JOURNAL.PCBI.1007239
citation: pmcid:PMC6705771
citation: pubmed:31437145
description: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins | A RESOURCE FOR FUSION PROTEINS AND THEIR INTERACTIONS | Milana Frenkel-Morgenstern's Cancer Genomics and BioComputing Lab at Bar-Ilan University, Israel | Result for the search by Unspecified: | Lars Juhl Jensen's Cellular Network Biology Group at The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark | ProtFus is a resource that has information about fusion proteins and their interactions, based on a text mining approach. "Tagging" is a process of registering the mention of given entities in a particular document | Text mining has been an active research topic for decades; however, it is only fairly recently that biomedical text-mining tools have been developed that make it practically applicable to a wide range of problems
feature list: operation_0306
feature list: operation 2492

ProtMapper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0218
application sub category: topic_0601
application sub category: topic_0602
citation: https://doi.org/10.1101/822668
description: Assembling a phosphoproteomic knowledge base using ProtMapper to normalize phosphosite information from databases and text mining. Map amino acid sites of post-translational modifications from models or data to reference positions. Code to generate results and figures relevant to the ProtMapper manuscript. The Protmapper maps references to protein sites to the human reference sequence based on UniProt, PhosphoSitePlus, and manual curation.
feature list: operation_0306
feature list: operation_0310
feature list: operation_0417
feature list: operation 3436
feature list: operation 3755
license: BSD-2-Clause

ProtMiscuity
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0821
application sub category: topic 3068
application sub category: topic 3489
application sub category: topic 3534
citation: BAZ103
citation: pmcid:PMC6813136
citation: pubmed:31650170
description: a database of promiscuous proteins. Promiscuous behaviour in proteins and enzymes remains a challenging feature to understand the structure-function relationship. Here we present ProtMiscuity, a manually curated online database of proteins showing catalytic promiscuity. ProtMiscuity contains information about canonical and promiscuous activities comprising 88 different reactions in 57 proteins from 40 different organisms. It can be searched or browsed by protein names, organisms and descriptions of canonical and promiscuous reactions. Entries provide information on reaction substrates, products and kinetic parameters, mapping of active sites to sequence and structure and links to external resources with biological and functional annotations.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3896

ProtRank
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0203
application sub category: topic 3520
citation: S12859-019-3144-3
citation: pmcid:PMC6842221
citation: pubmed:31706265
description: bypassing the imputation of missing values in differential expression analysis of proteomic data. Python package for differential abundance analysis of proteomics data
feature list: operation 2495
feature list: operation 3557
feature list: operation 3741
license: GPL-3.0

Protein-sol
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3306
application sub category: topic 3474
citation: https://doi.org/10.1101/625830
description: Solubility from protein sequence prediction.
feature list: operation_0409
feature list: operation 3435
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
software help: about

Protein Homeostasis Database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0121
application sub category: topic_0736
citation: btz628
citation: pmcid:PMC9883681
citation: pubmed:31392322
description: protein quality control in E. coli | Publicly available database regarding protein quality control in E. coli | You are using an unsupported browser. Please switch to recent version of either Chrome, Firefox, Edge, Opera or Safari
feature list: operation 2428
feature list: operation 3501

Proteo3Dnet
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
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input: UniProt accession
  type: FormalParameter
  additional type: data 3021
  encoding format: format 1957
output: PDB ID
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  additional type: data 1127
  encoding format: format 1957
output: UniProt accession
  type: FormalParameter
  additional type: data 3021
  encoding format: format 1957
output: BioGRID interaction ID
  type: FormalParameter
  additional type: data 2628
  encoding format: format 1957
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
  encoding format: format 3464
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic 2275
application sub category: topic 3510
description: Integration of structural information with interactomics data.
feature list: operation_0276
feature list: operation 3925
is accessible for free: true
license: Freeware
software help: Proteo3Dnet
software version: 1.02

ProteoClade
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3512
application sub category: topic 3520
citation: https://doi.org/10.1101/793455
description: a taxonomic toolkit for multi-species and metaproteomic analysis. ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimized for speed and storage requirements. What is ProteoClade? — ProteoClade 0.0.1 documentation. Free document hosting provided by Read the Docs
feature list: operation 3644
feature list: operation 3767
feature list: operation 3799
license: GPL-3.0
software help: proteoclade.readthedocs.io

ProteoRE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Workflow
application sub category: topic_0121
application sub category: topic 1775
application sub category: topic 2259
application sub category: topic 3360
citation: 978-1-0716-1641-3 11
citation: 978-1-4939-9164-8 18
citation: pubmed:30852829
citation: pubmed:34236662
description: ProteoRE (Proteomics Research Environment) is a Galaxy-based instance for the functional analysis and the exploration of proteomics and transcriptomics data in biomedical research; ProteoRE comprises 18 tools organized into five subsections for: i) data manipulation; ii) human and iii ) mouse species database annotation; iv) functional analysis; and v) pathway analysis along with graphical representations.
operating system: Linux
operating system: Mac
operating system: Windows
software version: 2.2

ProteoWorker
type: SoftwareApplication
input: Mass spectrometry spectra
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  additional type: data_0943
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  encoding format: format 3655
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic 3520
application sub category: topic 3557
description: Fully managed proteomics data analysis. Cloud-based proteomic data analysis that helps users go from raw MS data to results efficiently. Modern app + open source algorithms + powerful analysis tools
feature list: operation 3631
feature list: operation 3694
feature list: operation 3695
feature list: operation 3767
feature list: operation 3802
is accessible for free: false
license: Proprietary
operating system: Linux
operating system: Mac
operating system: Windows
software help: www.help.proteoworker.com
primary contact: https://orcid.org/0000-0001-9243-5084

ProteomeHD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic 2229
application sub category: topic 3474
application sub category: topic 3520
citation: s41587-019-0298-5
citation: pmcid:PMC6901355
citation: pubmed:31690884
description: ProteomeHD is an R script for creating a co-regulation map of the human proteome enables identification of protein functions.
feature list: operation 2495
feature list: operation 3216
feature list: operation 3638
feature list: operation 3766
feature list: operation 3767

Pseudo-nitzschia multistriata genome portal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0622
description: Web portal dedicated to the diatom Pseudo-nitzschia multistriata. A genome browser, a BLAST service and a download section are available.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

PsiZ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3474
citation: S13428-019-01285-3
citation: pmcid:PMC6797663
citation: pubmed:31432329
description: Obtaining psychological embeddings through joint kernel and metric learning | A python package for inferring psychological embeddings | PsiZ: A Psychological Embedding Package | Experiments using the PsiZ package published in Behavior Research Methods | PsiZ provides the computational tools to infer a continuous, multivariate stimulus representation using ordinal similarity relations. It integrates well-established cognitive theory with contemporary computational methods. The companion Open Access article is available at https://link.springer.com/article/10.3758/s13428-019-01285-3 | You will need a Python interpretter (>= 3.6) along with the an installation of the psiz package (version 0.1.0) in your preferred environment. You can install the correct version of the psiz package using pip: pip install psiz==0.1.0. You can also find version 0.1.0 on GitHub: https://github.com/roads/psiz/archive/v0.1.0.tar.gz
license: Apache-2.0

PsyMuKB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0128
application sub category: topic_0199
application sub category: topic_0749
application sub category: topic 3320
citation: j.gpb.2019.10.002
citation: pmcid:PMC6943783
citation: pubmed:31809863
description: An Integrative De Novo Variant Knowledge Base for Developmental Disorders. NeuroPsychiatric Mutation Knowledge Base. Welcome to our open access database PsyMuKB. PsyMuKB is a comprehensive knowledge base that links transcriptional and translational annotations to de novo variants, which are found in subjects but not in their parents, in developmental and neuropsychiatric disorders. Large-scale genomic and proteomic data are integrated into PsyMuKB, including developmental brain expressions, neuronal single-cell transcriptome, regulatory elements, and transcript annotations, protein-protein interactions (PPI) and protein isoform expressions. It aims to provide users with a comprehensive data exploration of de novo variants, such as their genomic locations on alternatively spliced isoforms, expression patterns of the mutation-disrupted genes and/or isoforms, and interaction network of impacted proteins
feature list: operation_0337
feature list: operation 3227

PubTator Central
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0218
application sub category: topic 3303
application sub category: topic 3473
citation: GKZ389
citation: pmcid:PMC6602571
citation: pubmed:31114887
description: Web-based application that provides computer-annotated biomedical concepts, such as genes and mutations, in PubMed citations and PMC full-text articles.
feature list: operation 2422
feature list: operation 3280
feature list: operation 3778
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: api.html
software help: tutorial.html
primary contact: https://orcid.org/0000-0002-8301-9553

PubTerm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0219
application sub category: topic_0621
application sub category: topic_0634
citation: bay137
citation: pmcid:PMC6323318
citation: pubmed:30624653
description: Web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records.
feature list: operation 2422
feature list: operation 3501
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: Pubterm Tutorial.pdf
software help: pubterm.html
primary contact: Victor Trevino

PulmonDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0219
application sub category: topic_0634
application sub category: topic 3308
citation: https://doi.org/10.1101/726745
description: a curated lung disease gene expression database | An accessible R package to download PulmonDB data | PulmonDB is a transcriptomic database of IPF and COPD with curated annotation | PulmonDB is a gene expression database with Chronic Obstructive Pulmonary Diseases (COPD) and Idiopathic Pulmonary Disease (IPF) experiments. It has homogenized values using individual contrast and manual curated annotation that can be download or accessed by http://pulmondb.liigh.unam.mx
feature list: operation_0224
feature list: operation 2495
feature list: operation 3258

Punchline
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic_0736
application sub category: topic 2830
application sub category: topic 3293
citation: https://doi.org/10.1101/686543
description: Punchline is a tool for identifying and comparing significant Pfam protein domain differences across draft whole genome sequences.
feature list: operation_0303
feature list: operation_0310
feature list: operation 2454

PureseqTM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0736
citation: https://doi.org/10.1101/627307
description: Efficient and accurate prediction of transmembrane topology from amino acid sequence only.
feature list: operation_0269
feature list: operation_0468
feature list: operation 2241
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

Py-EM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0611
application sub category: topic 3385
application sub category: topic 3452
citation: S41592-019-0396-9
citation: pubmed:31086343
description: Software tools for automated transmission electron microscopy.
feature list: operation 1812
feature list: operation 3457
feature list: operation 3552
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: readme.md
software help: https://git.embl.de/schorb/pyem/raw/master/pyEM.ipynb

PyAR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0166
application sub category: topic 3047
application sub category: topic 3314
citation: FCHEM.2019.00644
citation: pmcid:PMC6776882
citation: pubmed:31612127
description: A Global Optimizer for Nanoclusters. Python program for aggregation and reaction. PyAR stands for "Python program for aggregation and reaction"
feature list: operation 3432
feature list: operation 3435
feature list: operation 3436

PyBDA
type: SoftwareApplication
input: Matrix
  type: FormalParameter
  additional type: data 2082
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3391
citation: s12859-019-3087-8
description: A command-line tool for analysis of big biological data sets for distributed HPC clusters.
feature list: operation 2939
feature list: operation 2945
feature list: operation 3432
feature list: operation 3659
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: faq.html

PyBSASeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3168
citation: https://doi.org/10.1101/654137
description: Algorithm for BSA-Seq data analysis.
feature list: operation_0484
feature list: operation 3211
feature list: operation 3232
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

PyBioNetFit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 2259
application sub category: topic 2269
citation: j.isci.2019.08.045
citation: btac004
citation: pmcid:PMC10060707
citation: pmcid:PMC6744527
citation: pubmed:31522114
citation: pubmed:34986226
description: A general-purpose program for parameterizing biological models specified using the BioNetGen rule-based modeling language (BNGL) or the Systems Biology Markup Language (SBML).
feature list: operation 3799
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest

PyCellBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0749
citation: s12859-019-2726-4
citation: pmcid:PMC6438028
citation: pubmed:30922213
description: Python package for easy retrieval of biological data from heterogeneous sources.
feature list: operation 2422
is accessible for free: true
license: Apache-1.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 4.7.1
primary contact: Daniel Perez-Gil

PyDFN3D
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: PREPRINTS201911.0215.V1
description: Discontinuous Boundary Elements for Fluid Flow Problems in Discrete Fracture Networks. Modeling fluid flow in three-dimensional (3D) Discrete Fracture Networks (DFNs) is of relevance in many engineering applications, such as hydraulic fracturing, oil gas production, geothermal energy extraction, nuclear waste disposal and CO2 sequestration. A new Boundary Element Method (BEM) technique with discontinuous quadratic elements and a parallel Domain Decomposition Method (DDM) is presented herein for the simulation of the steady-state fluid flow in 3D DFN systems with wellbores, consisting of planar fractures having arbitrary properties and wellbore trajectories. Numerical examples characterized by DFNs of increasing complexity are investigated to evaluate the accuracy and efficiency of the presented technique.

PyFeat
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0082
application sub category: topic_0749
application sub category: topic 3512
citation: btz165
citation: pmcid:PMC6761934
citation: pubmed:30850831
description: Python-based effective feature generation tool for DNA, RNA and protein sequences.
feature list: operation_0440
feature list: operation 3092
feature list: operation 3798
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: PyFeat Manual.pdf
software help: README.md
primary contact: Rafsanjani Muhammod

PyGMQL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3382
application sub category: topic 3489
citation: S12859-019-3159-9
citation: pmcid:PMC6842186
citation: pubmed:31703553
description: scalable data extraction and analysis for heterogeneous genomic datasets. Python Library for data analysis based on GMQL. The doucumentation can be found at the following link: http://pygmql.readthedocs.io. API for calling interactively the GMQL Engine from Python
feature list: operation_0224
feature list: operation_0337
feature list: operation 3791
license: Apache-2.0

PyLandStats
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0610
application sub category: topic_0769
application sub category: topic 3372
citation: JOURNAL.PONE.0225734
citation: pmcid:PMC6894873
citation: pubmed:31805157
description: An open-source Pythonic library to compute landscape metrics. Open-source Python library to compute landscape metrics. Example notebooks of the PyLandStats library. Test and Deploy Your Code with Confidence. Test Coverage History & Statistics. PyLandStats documentation! — PyLandStats 2.0.0a1 documentation. Citation: Bosch M. 2019. "PyLandStats: An open-source Pythonic library to compute landscape metrics". PLOS ONE, 14(12), 1-19. doi.org/10.1371/journal.pone.0225734. Citation: Bosch M. 2019. "PyLandStats: An open-source Pythonic library to compute landscape metrics". Preprint available at bioRxiv. https://doi.org/10.1101/715052. Travis CI enables your team to test and ship your apps with confidence. Easily sync your projects with Travis CI and you'll be testing your code in minutes. Test code coverage history for martibosch/pylandstats. Open-source Pythonic library to compute landscape metrics within the PyData stack (NumPy, pandas, matplotlib...)
feature list: operation_0337
feature list: operation 2238
feature list: operation 3891
license: GPL-3.0
software help: pylandstats.readthedocs.io

PyParadigm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3343
application sub category: topic 3384
application sub category: topic 3444
citation: FNINF.2019.00059
citation: pmcid:PMC6698780
citation: pubmed:31456680
description: Python Library to Build Screens in a Declarative Way | Python library to develope paradigms for psychological experiments | PyParadigm is a small library to build paradigms for psychological experiments. It utilizes pygame, and is installable via pip | Welcome to PyParadigm — PyParadigm 0.1 documentation | PyParadigm is a small set of classes and functions designed to make it easy to write psychological paradigms in Python | PyParadigm takes another approach
feature list: operation 1816
license: MIT
software help: pyparadigm.readthedocs.io

PyRETIS 2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0176
application sub category: topic 3325
application sub category: topic 3332
citation: JCC.26112
citation: pubmed:31742744
description: An improbability drive for rare events. pyretis - Rare Event Simulations with python. PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based on transition interface sampling and replica exchange transition interface sampling .
feature list: operation_0337
feature list: operation 2476
feature list: operation 3799

PyRadiomics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic 2640
application sub category: topic 3384
citation: MP.13844
citation: pmcid:PMC6916323
citation: pubmed:31580484
description: PyRadiomics is an ontology-guided radiomics analysis workflow (O-RAW).
feature list: operation 1812
feature list: operation 3435
feature list: operation 3443

PyRanges
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0654
citation: BTZ615
citation: pubmed:31373614
description: > CORRECT NAME OF TOOL COULD ALSO BE 'AVAILABILITY:PyRanges' | efficient comparison of genomic intervals in Python | (beta) Performant Pythonic GenomicRanges | PyRanges are collections of intervals that support comparison operations (like overlap and intersect) and other methods that are useful for genomic analyses. The ranges can have an arbitrary number of meta-data fields, i.e. columns associated with them | PyRanges is in a beta state. We are extremely responsive to bug-reports, so if you have problems or come across unexpected behavior, please create an issue | GenomicRanges and genomic Rle-objects for Python | Feel free to ask questions of the type "how do I do X with pyranges?" on public forums like Stack Overflow, Bioinformatics Stack Exchange or Biostars. You can use endrebak85#gmail.com to point me to the question(s) | "Finally ... This was what Python badly needed for years." - Heng Li
feature list: operation 3802
license: MIT

PyRates
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3315
application sub category: topic 3474
citation: JOURNAL.PONE.0225900
citation: pmcid:PMC6913930
citation: pubmed:31841550
description: Python framework for rate-based neural simulations. PyRates is a framework for neural modeling and simulations, developed by Richard Gast and Daniel Rose at the Max Planck Institute of Human Cognitive and Brain Sciences, Leipzig, Germany. Max Planck Institute for Human Cognitive and Brain Sciences. Welcome to the PyRates documentation! — PyRates 0.7.1 documentation. Welcome to the PyRates documentation!¶. PyRates is a Python 3 tool for building rate-based neural models and performing numerical simulations of their dynamic behavior. Efficient software solutions for building and analyzing neural models are of tremendous value to the field of computational neuroscience. Open-source Python toolbox for rate-based neural modeling. PyRates requires an installation of Python >=3.6.1
feature list: operation_0337
feature list: operation 2497
feature list: operation 3562
feature list: operation 3907
license: GPL-3.0
software help: pyrates.readthedocs.io

PyRod
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic 2275
citation: ACS.JCIM.9B00281
citation: pubmed:31117512
description: Software developed to generate dynamic molecular interaction fields (dMIFs) and pharmacophore features based on analyzing the protein environment of water molecules in molecular dynamcis simulations.
feature list: operation_0244
feature list: operation_0482
feature list: operation 2476
is accessible for free: true
license: GPL-2.0
operating system: Linux
software help: wiki

PySpacell
type: SoftwareApplication
input: Image metadata
  type: FormalParameter
  additional type: data 3546
  encoding format: format 3752
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 3579
  encoding format: format 3603
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 3508
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2229
application sub category: topic 3172
application sub category: topic 3382
application sub category: topic 3520
citation: cyto.a.23955
citation: pubmed:31872957
description: PySpacell is a Python Package for Spatial Analysis of Cell Images. Technologies such as microscopy, sequential hybridization, and mass spectrometry enable quantitative single-cell phenotypic and molecular measurements in situ. Deciphering spatial phenotypic and molecular effects on the single-cell level is one of the grand challenges and a key to understanding the effects of cell-cell interactions and microenvironment. However, spatial information is usually overlooked by downstream data analyses, which usually consider single-cell read-out values as independent measurements for further averaging or clustering, thus disregarding spatial locations. With this work, we attempt to fill this gap. We developed a toolbox that allows one to test for the presence of a spatial effect in microscopy images of adherent cells and estimate the spatial scale of this effect.
feature list: operation 2238
feature list: operation 3435
feature list: operation 3443
feature list: operation 3552
feature list: operation 3799
feature list: operation 3891

PyVOL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0166
application sub category: topic 3047
citation: https://doi.org/10.1101/816702
description: a PyMOL plugin for visualization, comparison, and volume calculation of drug-binding sites. volume calculation and segmentation. PyVOL: Protein Pocket Visualization, Segmentation, and Characterization. PyVOL is a python library packaged into a PyMOL GUI for identifying protein binding pockets, partitioning them into sub-pockets, and calculating their volumes
feature list: operation_0337
feature list: operation_0387
feature list: operation 2575
license: MIT

Pyntheon
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0199
application sub category: topic_0601
citation: https://doi.org/10.1101/725846
description: A Functional Analysis Framework for Protein Modifications and Mutations of 83 Model Organisms | Pyntheon; A post translational modifications (PTMs) mapping tool for 87 different species, these PTMs are taken from a large array of popular lab specimens | we are presenting, Universal Functional PTMs Mapping Tool (Pyntheon) which maps post translational modifications (PTMs) present in the functional regions of proteins of almost all lab specimens that are popular among research community. From viruses to human, this tool includes 87 species (see species_id.txt) can help mapping the mutations to PTMs sites or give information about the PTMs present for a list of proteins (UniProt ID) of interest
feature list: operation_0331
feature list: operation_0417
feature list: operation 3755
license: MIT

PypeAmplicon
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3168
citation: https://doi.org/10.1101/772384
description: a step-by-step guide to obtain a reduced SNP set and a pipeline to automate data processing in the Antarctic Midge, Belgica antarctica | Pipeline to automate the processing of amplicon data | PypeAmplicon v1.0: Python pipeline for analysis of amplicon data | Wijeratne S & Pavinato VAC. (2018, November 17). PypeAmplicon: Python pipeline for analysis of amplicon data (Version v1.0). Zenodo. doi: http://doi.org/10.5281/zenodo.1490421
feature list: operation_0484
feature list: operation 3196
feature list: operation 3216
license: GPL-3.0

Pypreclin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3304
application sub category: topic 3384
application sub category: topic 3444
citation: J.NEUROIMAGE.2019.116353
citation: pubmed:31743789
description: An automatic pipeline for macaque functional MRI preprocessing. Non-human primate functional MRI (fMRI) is a growing field in neuroscience. However, there is no standardized method for monkey fMRI data analysis, specifically for data preprocessing. The preprocessing of monkey fMRI data is challenged by several technical and experimental specificities of the monkey research such as artifacts related to body movements or to intracranial leads. Here we propose to address these challenges by developing a new versatile pipeline for macaque fMRI preprocessing. We developed a Python module, Pypreclin, to process raw images using state of the art algorithms embedded in a fully automatic pipeline. To evaluate its robustness, we applied Pypreclin to fMRI data acquired at 3T in both awake and anesthetized macaques, with or without iron oxide contrast agent, using single loop or multichannel phased-array coils, combined or not with intracranial implanted electrodes.

Python Video Annotator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0092
description: PythonVideoAnnotator is a graphical application written in Python, to analyze and create notes for events in videos. It was developed with the aim of helping neuroscience and ethology researchers to identify animals’ behaviors based on the information extracted from the video.
feature list: operation_0226
feature list: operation_0337
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: pythonvideoannotator.readthedocs.io
software version: 3.306

Q-HIU
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0593
application sub category: topic_0634
citation: j.aca.2018.11.018
citation: pubmed:30661589
description: Quantitative hyperspectral image unmixing (Q-HIU) method is intended for quantitative data analysis of multi-set and individual Raman micro-spectroscopy images, allowing to efficiently retrieve non-negative spatial concentration maps and non-negative spectral profiles of the images’ chemical constituents (components) with no a priori information, minimum input parameters, and great operation speed.
feature list: operation 3799
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

QA4ECV FAPAR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3393
application sub category: topic 3810
citation: S19173662
citation: pmcid:PMC6749258
citation: pubmed:31443603
description: Can We Use Satellite-Based FAPAR to Detect Drought? | Quality Assurance for Essential Climate Variables | The FP7 QA4ECV project was initiated in 2014 to demonstrate how reliable and traceable quality information can be provided for satellite and ground-based measurements of climate and air quality parameters. The project developed and applied a Quality Assurance framework on new and improved multi-decadal data records of the Land ECVs Albedo, Leaf Area Index (LAI), and Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), and of the Atmosphere ECVs nitrogen dioxide (NO2), formaldehyde (HCHO), and carbon monoxide (CO) | We encourage you to browse through the website and survey the scope of QA4ECV activities

QBiC-Pred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0749
application sub category: topic 3169
citation: GKZ363
citation: pmcid:PMC6602471
citation: pubmed:31114870
description: Quantitative predictions of transcription factor binding changes due to sequence variants.
feature list: operation_0331
feature list: operation_0445
feature list: operation 3799
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
primary contact: Raluca Gordân

QC-ART
type: SoftwareApplication
input: Quality control report
  type: FormalParameter
  additional type: data 3914
  encoding format: format 2330
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 3603
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: A tool for real-time quality control assessment of mass spectrometry-based proteomics data.
feature list: operation 2238
feature list: operation 2940

QCMAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: PMIC.201900068
citation: pubmed:31099962
description: Web-Tool for Performance Diagnosis and Prediction of liquid chromatography-mass spectrometry (LC-MS) Systems.
feature list: operation 3633
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

QGIS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 3382
application sub category: topic 3489
citation: PEERJ.PREPRINTS.2127V2
citation: PEERJ.PREPRINTS.2209V2
citation: PEERJ.PREPRINTS.2243V2
description: QGIS is a free and open source Geographic Information System.
feature list: operation_0387
feature list: operation 3454
feature list: operation 3565

QHOT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 3517
citation: g3.118.200922
citation: pmcid:PMC6385979
citation: pubmed:30541929
description: Statistical procedure for genome-wide detection of QTL hotspots using public databases.
feature list: operation_0282
feature list: operation 3196
feature list: operation 3232
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: Usage of R code functions.(QHOT).docx
primary contact: Chen-Hung Kao

QMEANDisCo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0736
application sub category: topic 2275
application sub category: topic 3474
citation: btz828
citation: pmcid:PMC7075525
citation: pubmed:31697312
description: Distance Constraints Applied on Model Quality Estimation. QMEAN, the Qualitative Model Energy ANalysis, is a composite scoring function assessing the major geometrical aspects of protein structures. Estimates of structure quality are provided for full structures as well as on a local per residue scale. QMEAN Qualitative Model Energy ANalysis. QMEAN - Qualitative Model Energy ANalysis. Reference for the QMEANDisCo scoring function:. For optimum performance, please add the SEQRES of your model here. Merge branch 'release-3.1.0' · 3c2b6012. Local quality is either estimated using the raw QMEAN scoring function or one of the two specialized functions QMEANBrane and QMEANDisCo. They all provide scores in range [0,1] with one being good. Reference for the QMEAN scoring function:
feature list: operation_0321
feature list: operation_0477
feature list: operation 3435

QPA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0202
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic_0749
application sub category: topic 3519
citation: J.JEP.2019.112372
citation: pubmed:31683036
description: The roles of Qishen granules recipes, Qingre Jiedu, Wenyang Yiqi and Huo Xue, in the treatment of heart failure.
feature list: operation 2497
feature list: operation 3223
feature list: operation 3799

QPN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3305
application sub category: topic 3337
application sub category: topic 3384
application sub category: topic 3399
citation: jpd-191775
citation: pmcid:PMC7029361
citation: pubmed:31868683
description: A Researcher-Patient Matching Platform and Multimodal Biorepository. WELCOME TO QUEBEC PARKINSON NETWORK. Quebec Parkinson Network now allows researchers, clinicians and patients to regroup. Promoting collaboration of different actors in the fight against Parkinson's disease, the Network wants to be the new leader of the research on the disease. Support, act and help researchers and clinicians in the fight against Parkinson's disease by participating in research projects. For more information, visit the Participants section. Congress of the “Société Francophone Posture, Équilibre et Locomotion” (SOFPEL) – December 4 & 5, 2019
feature list: operation 3196
feature list: operation 3659

QRISK3
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3335
application sub category: topic 3422
application sub category: topic 3577
citation: F1000RESEARCH.21679.1
description: an unofficial research purposed implementation of ClinRisk’s QRISK3 algorithm into R. 10-Year Cardiovascular Disease Risk Calculator (QRISK3 2017). This function aims to calculate risk of developing cardiovascular disease of individual patients in next 10 years. The package was based on published risk prediction algorithm <https://qrisk.org/three/src.php>. A QRISK3 R package implements QRISK3 algorithm into R. Validation of CRAN R package "QRISK3". This respiratory provides the validation programs including QRISK3 SAS macro and original C function for CRAN package "QRISK3" for transparency and replication. Welcome to the QRISK ® 3-2018 risk calculator https://qrisk.org/three. This calculator is only valid if you do not already have a diagnosis of coronary heart disease (including angina or heart attack) or stroke/transient ischaemic attack
feature list: operation 2428
feature list: operation 3283
license: GPL-3.0

QResearch
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0102
application sub category: topic 3335
application sub category: topic 3399
citation: jhi.v12i1.108
citation: pubmed:15140353
description: General practice database for research.
feature list: operation 3283
feature list: operation 3557
is accessible for free: true
license: CC-BY-NC-SA-4.0
operating system: Linux
operating system: Mac
operating system: Windows

QS-Net
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0637
application sub category: topic 3293
citation: FGENE.2019.00607
citation: pmcid:PMC6667645
citation: pubmed:31396256
description: Reconstructing Phylogenetic Networks Based on Quartet and Sextet | User Manual for QS-Net Introduction The QS-Net is a phylogenetic network reconstruction method taking advantage of information on the relationship among six taxa
feature list: operation_0548
feature list: operation 3478
feature list: operation 3660
license: MIT

QSAR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3336
application sub category: topic 3375
application sub category: topic 3474
citation: S12859-019-3135-4
citation: pmcid:PMC6815455
citation: pubmed:31655545
description: Comprehensive ensemble in QSAR prediction for drug discovery. There exist a new type of QSAR individual classifier that is an end-to-end neural network model based on 1D-CNN and RNN. It extracts sequential features automatically from the SMILES.
feature list: operation 3436
feature list: operation 3659
feature list: operation 3799

QSAR-Co
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3343
citation: ACS.JCIM.9B00295
citation: pubmed:31083984
description: Software for Developing Robust Multitasking or Multitarget Classification-Based QSAR Models.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: manual-and-license
primary contact: Pravin Ambure

QSM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3379
application sub category: topic 3400
application sub category: topic 3444
citation: JON.12658
citation: pmcid:PMC6814493
citation: pubmed:31379055
description: Clinical Integration of Automated Processing for Brain Quantitative Susceptibility Mapping | Cornell MRI Research Lab Research Interests | Quantitative Susceptibility Mapping | Quantitative Susceptibility Mapping (QSM) provides a map of local tissue magnetic susceptibility
feature list: operation 3454
feature list: operation 3629
feature list: operation 3799

QTL-BSA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 3673
citation: S12539-019-00344-9
citation: pubmed:31388943
description: A Bulked Segregant Analysis and Visualization Pipeline for QTL-seq | In recent years, the application of Whole Genome Sequencing (WGS) on plants has generated sufficient data for the identification of trait-associated genomic loci or genes. A high-throughput genome-assisted QTL-seq strategy, combined with bulked-segregant analysis and WGS of two bulked populations from a segregating progeny with opposite phenotypic trait values, has gained increasing popularities in research community. However, there is no publicly available user friendly software for the identification and visualization. Hence, we developed a tool named QTL-BSA (QTL-bulked segregant analysis and visualization pipeline), which could facilitate the rapid identification and visualization of candidate QTLs from QTL-seq. As a proof-of-concept study, we have applied the tool for the rapid discovery and the identification of genes related with the partial blast resistance in rice
feature list: operation_0282
feature list: operation_0484
feature list: operation 3232

QTLbase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic 3173
application sub category: topic 3517
application sub category: topic 3518
citation: gkz888
citation: pmcid:PMC6943073
citation: pubmed:31598699
description: an integrative resource for quantitative trait loci across multiple human molecular phenotypes. QTLbase curates and compiles genome-wide QTL summary statistics for many human molecular traits across over 70 tissue/cell types. The database comprises tens of millions significant genotype-molecular trait associations under different conditions. Users can visualize QTL results in phenome-wide and tissue-wide levels, and annotate their biological functions through comprehensive genomic features and functional evidence. QTLbase provides a one-stop shop of QTLs retrieval and comparison across multiple tissues and multiple layers of molecular complexity, and it will greatly help researchers interrogate the biological mechanism of causal variants and guide the direction of functional validation
feature list: operation_0282
feature list: operation_0337
feature list: operation 2422
feature list: operation 3232
feature list: operation 3799

QTLpoly
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 3810
citation: https://doi.org/10.1101/622951
description: R package for random-effect multiple quantitative trait loci (QTL) mapping in autopolyploids.
feature list: operation_0282
feature list: operation 3196
feature list: operation 3232
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: 1-tutorial
primary contact: Guilherme da Silva Pereira

QUBEKit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic_0209
application sub category: topic 3047
citation: CHEMRXIV.7247045.V2
description: Automating the Derivation of Force Field Parameters from Quantum Mechanics. Modern molecular mechanics force fields are widely used for modelling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. For molecules outside the training set, parameters may be missing or inaccurate, and in these cases, it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines the latest QM parameter derivation methodologies with a novel method for deriving the positions and charges of off-center virtual sites.
feature list: operation 2476
feature list: operation 3893

QUBIC2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3518
citation: btz692
citation: pmcid:PMC8215922
citation: pubmed:31503285
description: A novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data | A novel biclustering algorithm for analyses of transcriptomic data | QUBIC2 is a novel biclustering algorithm for analyses of gene expression data from bulk and single-cell RNA-Sequencing. This introductory vignette provides an overview of installation and usage
feature list: operation 3501

QresFEP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic_0199
citation: ACS.JCTC.9B00538
citation: pubmed:31436990
description: > HOMEPAGE MISSING! | An Automated Protocol for Free Energy Calculations of Protein Mutations in Q | Predicting the effect of single-point mutations on protein stability or protein-ligand binding is a major challenge in computational biology. Free energy calculations constitute the most rigorous approach to this problem, though the estimation of converged values for amino acid mutations remains challenging. To overcome this limitation, we developed tailored protocols to calculate free energy shifts associated with single-point mutations. We herein describe the QresFEP protocol, which includes an extension of our recent protocols to cover all amino acids mutations, based on the latest versions of the OPLS-AA force field. QresFEP is implemented in an application programming interface framework and the graphic interface QGui, for the molecular dynamics software Q
feature list: operation_0480
feature list: operation_0482

QuAdTrim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3168
citation: https://doi.org/10.1101/2019.12.18.870642
description: Overcoming computational bottlenecks in sequence quality control. Abstract With the recent torrent of high throughput sequencing (HTS) data the necessity for highly efficient algorithms for common tasks is paramount. One task for which the basis for all further analysis of HTS data is initial data quality control, that is, the removal or trimming of poor quality reads from the dataset. Here we present QuAdTrim, a quality control and adapter trimming algorithm for HTS data that is up to 57 times faster and uses less than 0.06% of the memory of other commonly used HTS quality control programs. QuAdTrim will reduce the time and memory required for quality control of HTS data, and in doing, will reduce the computational demands of a fundamental step in HTS data analysis. Additionally, QuAdTrim impliments the removal of homopolymer Gs from the 3’ end of sequence reads, a common error generated on the NovaSeq, NextSeq and iSeq100 platforms
feature list: operation 3192
feature list: operation 3218
feature list: operation 3237
license: BSD-3-Clause

QuantiMus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3382
application sub category: topic 3474
citation: FPHYS.2019.01416
citation: pmcid:PMC6895564
citation: pubmed:31849692
description: A Machine Learning-Based Approach for High Precision Analysis of Skeletal Muscle Morphology. QuantiMus is a machine-learning based program used for histological analysis of skeletal muscle. Developed as a plugin for the image analysis tool flika, QuantiMus is a versatile, fast, and precise to complete histological analysis. QuantiMus is written in Python and is open-source
feature list: operation_0337
feature list: operation 3443

QuantileBootstrap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3336
application sub category: topic 3474
citation: btz293
citation: pmcid:PMC6853675
citation: pubmed:31070704
description: Decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery.
feature list: operation 3216
feature list: operation 3659
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: James A. Watson

Quantum++
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3570
citation: journal.pone.0208073
citation: pmcid:PMC6287823
citation: pubmed:30532140
description: Modern general-purpose multi-threaded quantum computing library.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: wiki

QuantumATK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3314
application sub category: topic 3315
application sub category: topic 3318
citation: AB4007
citation: pubmed:31470430
description: an integrated platform of electronic and atomic-scale modelling tools | QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals
feature list: operation 3216
feature list: operation 3891

QuartetScores
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0194
application sub category: topic 3293
citation: SYZ058
citation: pubmed:31504977
description: Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence | Code for computing various support scores for internodes | See http://www.biorxiv.org/content/early/2017/07/27/168526 for the preprint | If you cannot find our supplementary text, please download it from here: https://github.com/lutteropp/QuartetScores/issues/4
feature list: operation_0323
feature list: operation_0325
feature list: operation_0552
license: GPL-3.0

Query Tabular
type: SoftwareApplication
input: Text
  type: FormalParameter
  additional type: data 3671
  encoding format: format 3475
output: Text
  type: FormalParameter
  additional type: data 3671
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic_0769
author: James E. Johnson
citation: f1000research.16450.2
citation: pmcid:PMC6248266
citation: pubmed:30519459
description: Query Tabular is a Galaxy-based tool which manipulates tabular files. Query Tabular automatically creates a SQLite database directly from a tabular file within a Galaxy workflow. The SQLite database can be saved to the Galaxy history, and further process to generate tabular outputs containing desired information and formatting.
feature list: operation_0224
feature list: operation 1812
feature list: operation 2409
feature list: operation 3695
license: CC-BY-4.0

Quetzal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0610
application sub category: topic 3855
citation: https://doi.org/10.1111/1755-0998.12992
citation: pubmed:30637945
description: Collection of C++ code snippets, that can be picked and combined to build complex, spatially explicit population genetics simulators and inference frameworks.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Arnaud Becheler

QuiC
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3710
  encoding format: format 3712
  encoding format: format 3858
output: Quality control report
  type: FormalParameter
  additional type: data 3914
  encoding format: format 3508
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: QuiC generates quality control metrics for liquid chromatography and mass spectrometry in near real-time from raw files from various vendors and bottom-up proteomics workflows using a commercially available standard. Requires Biognosys iRT Kit to enable automated, fast and accurate QC monitoring of your data sets.
feature list: operation 2428
feature list: operation 3628

QuickNII
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3304
application sub category: topic 3384
application sub category: topic 3444
author: Neural Systems Laboratory
citation: JOURNAL.PONE.0216796
citation: pmcid:PMC6541252
citation: pubmed:31141518
description: Tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.
feature list: operation 3552
funder: Horizon 2020
is accessible for free: true
license: CC-BY-NC-SA-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: quicknii-and-visualign
software help: quicknii.readthedocs.io
primary contact: 0000-0001-7899-906X

Quokka
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic_0601
citation: bty522
citation: pmcid:PMC6289136
citation: pubmed:29947803
description: Tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.
feature list: operation_0417
feature list: operation 3659
feature list: operation 3755
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Fuyi Li

R-BIND
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic_0632
application sub category: topic_0659
application sub category: topic 2258
citation: ACSCHEMBIO.9B00631
citation: pmcid:PMC6925312
citation: pubmed:31589399
description: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes. R-BIND: The RNA-Targeted BIoactive ligaNd Database. The dataset includes only bioactive ligands with demonstrated activity in cell culture and/or animal models. This database is expected to expedite the discovery of RNA chemical probes. R-BIND was created by the Hargrove Lab at Duke University
feature list: operation_0337
feature list: operation 2421
feature list: operation 2422

R2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic 3518
citation: FMED.2019.00237
citation: pmcid:PMC6831549
citation: pubmed:31737636
description: R2 is a biologist friendly web based genomics analysis and visualization application
feature list: operation_0337
feature list: operation 2436
feature list: operation 3463

RAACBook
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0736
application sub category: topic 3474
citation: BAZ131
citation: pmcid:PMC6893003
citation: pubmed:31802128
description: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule. Recently, the success of AlphaFold on creating 3D protein models demonstrates sequence-dependent inference plays a crucial role in computational proteomics. A web server of reduced amino acid alphabet for sequence-dependent inference
feature list: operation_0267
feature list: operation_0418
feature list: operation_0477

RACE-SEQ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic 3168
application sub category: topic 3512
citation: 978-1-4939-9670-4 17
citation: pubmed:31410804
description: RACE-SEQ and Population-Wide Polymorphism Susceptibility Testing for Endonucleolytically Active, RNA-Targeting Therapeutics | Pipeline for the downstream analysis of 5-RACE Next Generation Sequencing experiments | This is a custom R script for the downstream analysis of RACE-seq data | To run the RACE-SEQ-lite script you will need to have an R version ( >=3.4) installed on your system. All the necessary R packages will get installed and loaded automatically
feature list: operation_0465
feature list: operation 2008
feature list: operation 3192

RACS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic 3169
application sub category: topic 3170
application sub category: topic 3179
application sub category: topic 3316
citation: S12859-019-3100-2
citation: pmcid:PMC6819487
citation: pubmed:31664892
description: rapid analysis of ChIP-Seq data for contig based genomes. RACS: Rapid Analysis of ChIP-Seq data for contig based genomes -- repository
feature list: operation 3192
feature list: operation 3211
feature list: operation 3216
feature list: operation 3222
feature list: operation 3431

RADAR-base
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic 3419
citation: https://doi.org/10.2196/11734
citation: pmcid:PMC6694732
citation: pubmed:31373275
description: Open Source Mobile Health Platform for Collecting, Monitoring, and Analyzing Data Using Sensors, Wearables, and Mobile Devices | BACKGROUND:With a wide range of use cases in both research and clinical domains, collecting continuous mobile health (mHealth) streaming data from multiple sources in a secure, highly scalable, and extensible platform is of high interest to the open source mHealth community. The European Union Innovative Medicines Initiative Remote Assessment of Disease and Relapse-Central Nervous System (RADAR-CNS) program is an exemplary project with the requirements to support the collection of high-resolution data at scale; as such, the Remote Assessment of Disease and Relapse (RADAR)-base platform is designed to meet these needs and additionally facilitate a new generation of mHealth projects in this nascent field
feature list: operation_0337
feature list: operation 1812
feature list: operation 3431

RADProc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3673
application sub category: topic 3796
citation: https://doi.org/10.1111/1755-0998.12954
citation: pubmed:30312001
description: Computationally efficient de novo locus assembler for population studies using RADseq data.
feature list: operation_0476
feature list: operation 3196
feature list: operation 3644
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
primary contact: Dr. Beiko's Lab

RAEdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0749
application sub category: topic 3071
application sub category: topic 3512
citation: bay140
citation: pmcid:PMC6323319
citation: pubmed:30624654
description: Database of enhancers identified by high-throughput reporter assays.
feature list: operation_0224
feature list: operation_0438
feature list: operation 3501
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Dr. Yousong Peng

RAG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0099
citation: btz611
citation: pmcid:PMC7999136
citation: pubmed:31373604
description: Webserver for RNA structure prediction and design corresponding to tools developed using our RNA-As-Graphs (RAG) approach.
feature list: operation_0278
feature list: operation_0502
feature list: operation 2441

RAM-ESVM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0099
application sub category: topic 3168
application sub category: topic 3308
citation: ELZ018
citation: pubmed:31609411
description: A comprehensive comparison and analysis of computational predictors for RNA N6-methyladenosine sites of Saccharomyces cerevisiae.
feature list: operation 2426

RAMPAGE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic_0798
application sub category: topic 3277
citation: GR.249789.119
citation: pmcid:PMC6724667
citation: pubmed:31413151
description: > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'Alu', 'III-transcribed', 'Pol III-transcribed', 'III-transcribed Alu' | Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function | Pipeline to identify expressed Alu elements using RAMPAGE | A schematic flow shows the pipeline
feature list: operation_0441
feature list: operation_0443
feature list: operation 3232
license: MIT

RANKS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3293
citation: btw235
citation: pubmed:27256314
description: Tool for node label ranking and classification in biological networks.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: RANKS.pdf
primary contact: Giorgio Valentini

RAPPAS
type: SoftwareApplication
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
input: Species tree
  type: FormalParameter
  additional type: data 3272
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic_0637
application sub category: topic 3174
application sub category: topic 3293
author: Benjamin Linard
citation: btz068
citation: pubmed:30698645
description: RAPPAS stands for Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences. It uses an alignment-free approach for phylogenetic placement, thus removing the hurdle of query sequence alignment.
feature list: operation 3460
is accessible for free: true
operating system: Linux
software help: RAPPAS
software version: 1.2

RARe
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Data reference
  type: FormalParameter
  additional type: data 2093
output: Identifier
  type: FormalParameter
  additional type: data_0842
output: Database search results
  type: FormalParameter
  additional type: data 2080
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
additional type: Web application
additional type: Web service
application sub category: topic_0091
application sub category: topic_0610
application sub category: topic_0780
application sub category: topic 3071
application sub category: topic 3810
description: RARe is a research infrastructure registered on the french national roadmap that brings together five networks of BRCs conserving genetic, genomic, and biological resources assembled and characterized by research on domestic animals, model or cultivated plants, wild species related to domestic animals, forest trees, micro-organisms of agronomic or agri-food interest, micro-organisms and environmental organisms. The purpose of this web portal is to facilitate the discoverability of these data. RARe search is an implementation of DataDiscovery.
feature list: operation_0227
feature list: operation 2421
feature list: operation 3625
feature list: operation 3908
is accessible for free: true
license: BSD-3-Clause
software help: about
software help: help
software help: join
software help: legal
primary contact: Support service

RASflow
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic_0769
application sub category: topic 3170
citation: https://doi.org/10.1101/839191
description: An RNA-Seq Analysis Workflow with Snakemake. RASflow: RNA-Seq Analysis Snakemake Workflow
feature list: operation 3258
feature list: operation 3680
feature list: operation 3800
license: MIT

RAbHIT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic_0654
application sub category: topic 2830
citation: btz481
description: R Haplotype Antibody Inference Tool, that implements a novel algorithm to infer V(D)J haplotypes by adapting a Bayesian framework.
feature list: operation_0487
feature list: operation_0495
feature list: operation 3196
is accessible for free: true
license: CC-BY-SA-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: rabhit.pdf
software help: README.html
software help: RAbHIT-vignette.pdf
software version: 0.1.1
primary contact: Ayelet Peres

RAxML-NG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0194
application sub category: topic 3293
application sub category: topic 3810
citation: btz305
citation: pmcid:PMC6821337
citation: pubmed:31070718
description: Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.
feature list: operation_0547
feature list: operation_0552
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: wiki
software version: 0.8.0 beta
primary contact: Vital-IT helpdesk

RBP-Maps
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3320
application sub category: topic 3512
application sub category: topic 3794
citation: rna.069237.118
citation: pmcid:PMC6348990
citation: pubmed:30413564
description: Enables robust generation of splicing regulatory maps and rapid query of regulatory patterns of RNA binding protein (RBP) of interest.
feature list: operation_0232
feature list: operation_0264
feature list: operation_0433
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
primary contact: Yeo LAB

RBPome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0602
application sub category: topic 3047
application sub category: topic 3520
citation: J.ISCI.2019.11.039
citation: pmcid:PMC6926210
citation: pubmed:31835171
description: RBP atlas is an interactive online data mining tool.
feature list: operation_0303
feature list: operation 2436
feature list: operation 3196

RBV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic 3518
application sub category: topic 3577
application sub category: topic 3673
application sub category: topic 3676
citation: S41598-019-53181-7
citation: pmcid:PMC6858463
citation: pubmed:31729446
description: tool for prioritising copy number variations in germline conditions. Validating copy number variants from using allele balance from NGS data. RBV: Read Balance Validator is a corroborates copy number variants (CNV) from whole exome and whole genome sequence data. It uses the relative reads for the reference and alternative allele at a given position (the read balance) to determine the probability that a putative CNV is real
feature list: operation 2428
feature list: operation 3226
feature list: operation 3227
license: GPL-3.0

RCMF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0634
application sub category: topic_0749
citation: S12859-019-3260-0
citation: pmcid:PMC6929455
citation: pubmed:31874608
description: RCMF is a robust collaborative matrix factorization method to predict miRNA-disease associations.
feature list: operation 3435

RCSM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0202
application sub category: topic_0203
application sub category: topic 3295
application sub category: topic 3336
application sub category: topic 3518
citation: BBZ129
citation: pubmed:31774912
description: RCSM(Recommended Connectivity-map Scoring Methods) is a comprehensive evaluation of connectivity methods for L1000 data.
feature list: operation 2495
feature list: operation 3435
feature list: operation 3799

RDFIO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: SPARQL endpoint
application sub category: topic 3071
application sub category: topic 3172
application sub category: topic 3325
citation: s13326-017-0136-y
citation: pmcid:PMC5584330
citation: pubmed:28870259
description: Extends the RDF import and export functionality in Semantic MediaWiki (SMW) to enable using SMW as a collaborative platform for editing semantic data.
feature list: operation_0337
feature list: operation 3096
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: RDFIO
software help: Extension:RDFIO

RDKit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0209
application sub category: topic 2258
application sub category: topic 3047
citation: CHEMRXIV.7791947.V2
description: RDKit is an Open-Source Cheminformatics Software. Fast, Efficient Fragment-Based Coordinate Generation for Open Babel.
feature list: operation_0475
feature list: operation 1844
feature list: operation 2476

RDXplorer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3673
citation: gr.092981.109
citation: journal.pcbi.1007069
citation: pmcid:PMC2752127
citation: pmcid:PMC6555534
citation: pubmed:19657104
citation: pubmed:31136576
description: > TOOL (matuskalas) | Comprehensively benchmarking applications for detecting copy number variation | The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group Note: (matuskalas): Lumpy (or lumpy-sv) is a completely different tool, atm missing in bio.tools (https://github.com/arq5x/lumpy-sv)
feature list: operation 3196
feature list: operation 3227
feature list: operation 3230
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
software help: rdxplorer.sourceforge.net
primary contact: Makarov V.

REFUGE Challenge
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3360
application sub category: topic 3384
application sub category: topic 3417
application sub category: topic 3474
citation: J.MEDIA.2019.101570
citation: pubmed:31630011
description: A unified framework for evaluating automated methods for glaucoma assessment from fundus photographs. The goal of the Retinal Fundus Glaucoma Challenge (REFUGE) is to evaluate and compare automated algorithms for glaucoma detection and optic disc/cup segmentation on a common dataset of retinal fundus images.
feature list: operation 3283
feature list: operation 3443
feature list: operation 3553

REPIC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3168
application sub category: topic 3295
application sub category: topic 3308
application sub category: topic 3512
citation: https://doi.org/10.1101/2019.12.11.873299
description: A database for exploring N6-methyladenosine methylome. REPIC (RNA Epitranscriptome Collection) is a database dedicated to provide a new resource to investigate potential functions and mechanisms of N6-adenosine methylation (m6A) modifications. Currently, The database includes about 700 samples of 50 public studies that were reprocessed by our refined pipeline. The database also contains ENCODE histone ChIP-seq and DNase-seq data to correlate m6A modifications. It provided multi-dimensional information (e.g. cell or tissue specificity) to query m6A modification relevance in cellular processes. In addition, a built-in modern genome browser presented a comprehensive atlas of m6A modifications which is helpful to visualize m6A modification sites between different samples and conditions.
feature list: operation_0224
feature list: operation 3208
feature list: operation 3222

RERconverge
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0084
application sub category: topic_0625
author: Amanda Kowalczyk
author: Maria Chikina
author: Nathan Clark
author: Raghavendran Partha
author: Weiguang (Wayne) Mao
author: Wynn Meyer
citation: btz468
citation: pmcid:PMC6853647
citation: pubmed:31192356
description: R package for associating evolutionary rates with convergent traits.
feature list: operation_0547
feature list: operation_0554
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: RERconverge-master.pdf
primary contact: Maria Chikina
primary contact: Nathan Clark
primary contact: Raghavendran Partha
primary contact: Weiguang (Wayne) Mao
primary contact: Wynn Meyer

RESTORE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 2830
application sub category: topic 3360
application sub category: topic 3382
application sub category: topic 3518
citation: https://doi.org/10.1101/792770
description: Robust intEnSiTy nORmalization mEthod for Multiplexed Imaging.
feature list: operation 3435
feature list: operation 3799

RFQAmodel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0130
application sub category: topic_0736
citation: JOURNAL.PONE.0218149
citation: pmcid:PMC6802825
citation: pubmed:31634369
description: Random Forest Quality Assessment to identify a predicted protein structure in the correct fold.
feature list: operation_0272
feature list: operation_0303
feature list: operation_0321
feature list: operation_0474

RF_Purify
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 3295
application sub category: topic 3518
citation: S12859-019-3014-Z
citation: pmcid:PMC6697926
citation: pubmed:31419933
description: a novel tool for comprehensive analysis of tumor-purity in methylation array data based on random forest regression | RF model and functions to estimate tumor purity using methylation data | Install minfi and RF_purify package from GitHub | R-package to predict ABSOLUTE and ESTIMATE tumor purity using a Random Forest regression model trained on TCGA Illumina 450k DNA-methylation array data. Purity prediction functions can be applied to 450k and 850k array data preprocessed with the Bioconductor package minfi
feature list: operation_0430
feature list: operation 3233
feature list: operation 3659

RGAAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 3168
citation: j.gpb.2018.03.006
citation: pmcid:PMC6364042
citation: pubmed:30583062
description: Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes.
feature list: operation_0525
feature list: operation 3209
feature list: operation 3227
is accessible for free: true
license: Unlicense
operating system: Linux
primary contact: Qiang Lin

RGADE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 3810
citation: S12864-019-6207-Y
citation: pmcid:PMC6836459
citation: pubmed:31694536
description: RGADE is a tool with genomic features and differential expression of the innate immune system from a smut-resistant genotype.
feature list: operation_0303
feature list: operation_0524
feature list: operation 3196
feature list: operation 3432

RGRPT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic_0654
application sub category: topic 3293
citation: FGENE.2019.01020
citation: pmcid:PMC6828935
citation: pubmed:31737036
description: RGRPT is a New Algorithm for Identifying Genome Rearrangements in the Mammalian Evolution. Genome rearrangements are the evolutionary events on level of genomes. It is a global view on evolution research of species to analyze the genome rearrangements. We introduce a new method called RGRPT (recovering the genome rearrangements based on phylogenetic tree) used to identify the genome rearrangements. We test the RGRPT using simulated data. The results of experiments show that RGRPT have high sensitivity and specificity compared with other tools when to predict rearrangement events. We use RGRPT to predict the rearrangement events of six mammalian genomes (human, chimpanzee, rhesus macaque, mouse, rat, and dog). RGRPT has recognized a total of 1,157 rearrangement events for them at 10 kb resolution, including 858 reversals, 16 translocations, 249 transpositions, and 34 fusions fissions.
feature list: operation_0323
feature list: operation_0326
feature list: operation_0567
feature list: operation 3745

RHPCG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3173
application sub category: topic 3512
citation: BAZ135
citation: pmcid:PMC6917511
citation: pubmed:31848596
description: a database of the Regulation of the Hippo Pathway in Cancer Genome. Hippo signaling pathway is a highly conserved pathway, which is consisted of a group of kinases. Dysregulation of Hippo signaling pathway is involved in the initiation and progression of cancer, such as breast cancer, lung cancer and so on. RHPCG serves as a valuable resource for understanding the roles of Hippo signaling pathway in carcinogenesis. The features of RHPCG contain: (i) the landscape of Hippo gene alterations at multiple omics level; (ii) quick search Hippo regulatory motifs by mRNA, lncRNA, circRNA or miRNA; and (iii) all the Hippo related motifs can be visualized as network and be downloaded freely
feature list: operation_0239
feature list: operation 2495
feature list: operation 3083
feature list: operation 3439

RICE-GUARD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic_0780
application sub category: topic 3474
citation: S12859-019-3065-1
citation: pmcid:PMC6806664
citation: pubmed:31640541
description: The RICE-GUARD project will develop a wireless sensor network comprised of low-cost measurement nodes that will be capable of transmitting readings of the relevant in-field site-specific environmental variables in real-time to a central server. Rice blast is the most serious disease of cultivated rice. It is caused by the fungus Magnaporthe grisea (Pyricularia oryzae Cav.), which in favourable conditions can produce yield losses of up to 100 %. Although rice blast is present wherever rice is cultivated, its intensity (incidence and severity of disease) is highly variable and depends on cropping system and climate.
feature list: operation 3435

RICOPILI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3316
application sub category: topic 3517
citation: btz633
citation: pmcid:PMC7868045
citation: pubmed:31393554
description: Rapid Imputation for COnsortias PIpeLIne | Rapid Imputation and COmputational PIpeLIne for Genome-Wide Association Studies | RICOPILI: Rapid Imputation and COmputational PIpeLIne for Genome-Wide Association Studies by Stephan Ripke is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Based on a work at https://sites.google.com/a/broadinstitute.org/ricopili/download
feature list: operation 3557
feature list: operation 3891

RIL-Contour
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3474
citation: s10278-019-00232-0
citation: pmcid:PMC6646456
citation: pubmed:31089974
description: Medical Imaging Dataset Annotation Tool for and with Deep Learning.
feature list: operation 2422
feature list: operation 3553
feature list: operation 3778
is accessible for free: true
license: BSD-2-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

RINspector
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic_0130
application sub category: topic_0199
application sub category: topic_0736
citation: btx586
citation: f1000research.14298.2
citation: pmcid:PMC5860209
citation: pmcid:PMC5998007
citation: pubmed:29028877
citation: pubmed:29946443
description: Combines centrality analyses of Residue Interaction Networks (RIN) with DynaMine flexibility predictions.
feature list: operation_0248
feature list: operation 2406
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: cpbi.66
software version: 1.3.0
primary contact: https://orcid.org/0000-0002-6807-6621

RIPTiDe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 3308
application sub category: topic 3407
citation: https://doi.org/10.1101/637124
description: Transcriptomic analyses of bacteria have become instrumental to our understanding of their responses to changes in their environment.
feature list: operation 3629
feature list: operation 3660
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Matthew L. Jenior

RIPper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0749
application sub category: topic 3794
citation: PEERJ.7447
citation: pmcid:PMC6714961
citation: pubmed:31523495
description: web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations | The RIPper is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in genome sequences of Ascomycota | The RIPper was built using Asp.Net Core with an AngularJs based front-end and uses session storage to keep a users files for a defined amount of time. The RIPper has no account or database requirements
feature list: operation 3216
feature list: operation 3799
license: GPL-3.0

RIdeogram
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0654
application sub category: topic 3295
citation: PEERJ-CS.251
citation: pmcid:PMC7924719
citation: pubmed:33816903
description: drawing SVG graphics to visualize and map genome-wide data on the idiograms | Drawing SVG Graphics to Visualize and Map Genome-Wide Data on Idiograms | For whole-genome analysis, idiograms are virtually the most intuitive and effective way to map and visualize the genome-wide information. RIdeogram was developed to visualize and map whole-genome data on idiograms with no restriction of species | RIdeogram is a R package to draw SVG graphics to visualize and map genome-wide data on idiograms (Scalable Vector Graphics http://tutorials.jenkov.com/svg/index.html)
feature list: operation_0575
feature list: operation 2429
license: Artistic-2.0
primary contact: Guangchuang Yu
primary contact: Jinhui Chen

RIscoper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0218
application sub category: topic_0659
application sub category: topic 3512
description: Tool for RNA–RNA interaction extraction from the literature.
feature list: operation_0306
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: document.html
primary contact: Wang Dong

RMBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0659
application sub category: topic 3320
application sub category: topic 3512
citation: gkx934
citation: pmcid:PMC5753293
citation: pubmed:29040692
description: Database to integrate epitranscriptome sequencing data for exploring post-transcriptionally modifications of RNAs, as well as their relationships with microRNA binding events, disease-related SNPs and RNA-binding proteins (RBP).
feature list: operation_0417
feature list: operation 2495
feature list: operation 3196
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 2.0
primary contact: Jian-Hua Yang

RMKL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3474
citation: S12859-019-2992-1
citation: pmcid:PMC6694479
citation: pubmed:31416413
description: Multiple-kernel learning for genomic data mining and prediction | Multiple Kernel Learning for Classification or Regression Problems | Provides R and C++ function that enable the user to conduct multiple kernel learning (MKL) and cross validation for support vector machine (SVM) models. Cross validation can be used to identify kernel shapes and hyperparameter combinations that can be used as candidate kernels for MKL. There are three implementations provided in this package, namely SimpleMKL Alain Rakotomamonjy et. al (2008), Simple and Efficient MKL Xu et. al (2010), and Dual augmented Lagrangian MKL Suzuki and Tomioka (2011) <doi:10.1007/s10994-011-5252-9>. These methods identify the convex combination of candidate kernels to construct an optimal hyperplane
feature list: operation_0306
feature list: operation_0463
feature list: operation 3659
license: GPL-3.0

RMut
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic 3336
citation: journal.pone.0213736
citation: pmcid:PMC6424452
citation: pubmed:30889216
description: R package for a Boolean sensitivity analysis against various types of mutations.
feature list: operation 3202
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: RMut Tutorial.pdf
software help: Readme.md

RNA-seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0202
application sub category: topic_0203
application sub category: topic_0634
application sub category: topic 3170
application sub category: topic 3512
citation: https://doi.org/10.1101/813980
description: A transcriptional toolbox for exploring peripheral neuro-immune interactions. Abstract Correct communication between immune cells and peripheral neurons is crucial for the protection of our bodies. Its breakdown is observed in many common, often painful conditions, including arthritis, neuropathies and inflammatory bowel or bladder disease. Here, we have characterised the immune response in a mouse model of neuropathic pain using flow cytometry and cell-type specific RNA sequencing (RNA-seq). We found few striking sex differences, but a very persistent inflammatory response, with increased numbers of monocytes and macrophages up to 3½ months after the initial injury. This raises the question of whether the commonly used categorisation of pain into “inflammatory” and “neuropathic” is one that is mechanistically appropriate. Finally, we collated our data with other published RNA-seq datasets on neurons, macrophages and Schwann cells in naïve and nerve injury states
feature list: operation 3563
feature list: operation 3565
feature list: operation 3800

RNAIndel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2885
application sub category: topic 3170
application sub category: topic 3474
citation: btz753
citation: pmcid:PMC7523641
citation: pubmed:31593214
description: discovering somatic coding indels from tumor RNA-Seq data. Somatic indel discovery tool for tumor RNA-Seq data. RNAIndel calls coding indels from tumor RNA-Seq data and classifies them as somatic, germline, and artifactual. You can also use RNAIndel as a postprocessor to classify indels called by your own caller. RNAIndel supports GRCh38 and 37
feature list: operation_0226
feature list: operation_0452
feature list: operation 3435
is accessible for free: true
license: Apache-2.0
software help: RNAIndel
software version: 2.2.2

RNARedPrint
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0097
application sub category: topic_0099
application sub category: topic_0154
citation: s12859-019-2784-7
citation: pmcid:PMC6482512
citation: pubmed:31023239
description: Fixed-parameter tractable sampling for RNA design with multiple target structures.
feature list: operation_0278
feature list: operation_0502
feature list: operation_0570
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Yann Ponty

RNASeq_similarity_matrix
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3170
application sub category: topic 3382
citation: BTZ821
citation: pubmed:31769800
description: visually identify sample mix-ups in RNASeq data using a 'genomic' sequence similarity matrix. A pipeline to detect sample mix-ups in RNASeq data. Generate a sample similarity matrices from RNASeq data. Sample confusion is a common laboratory problem. In RNASeq this is frequently tested for by checking whether sex-specific genes (e.g. those located on the Y chromosome or the X inactivation gene) are congruent with the sex listed for that sample in the metadata. However, this method cannot be used to detect sample confusion between patients of the same sex, and is less sensitive when the phenotype skews the sex ratio of samples away from 1:1. Here we present a tool that leverages RNASeq reads to call genomic SNPs, and use that to generate a similarity matrix between all samples to detect sample confusion. git clone https://github.com/nicokist/RNASeq_similarity_matrix
feature list: operation_0337
feature list: operation_0484
feature list: operation 3802
license: GPL-3.0

RNATracker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3474
application sub category: topic 3512
citation: BTZ337
citation: pmcid:PMC6612824
citation: pubmed:31510698
description: Prediction of mRNA subcellular localization using deep recurrent neural networks | RNATracker is a deep learning approach to learn mRNA subcellular localization patterns and to infer its outcome. It operates on the cDNA of the longest isoformic protein-coding transcript of a gene with or without its corresponding secondary structure annnotations. The learning targets are fractions/percentage of the transcripts being localized to a fixed set of subcellular compartments of interest
feature list: operation_0441
feature list: operation_0443
feature list: operation 2489
license: GPL-3.0

RNAactDrug
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0208
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3047
application sub category: topic 3512
citation: BBZ142
citation: pubmed:31799597
description: a comprehensive database of RNAs associated with drug sensitivity from multi-omics data. RNAactDrug a comprehensive database of RNAs associated with Drug sensitivity from multi-omics data. RNAactDrug is a comprehensive resource for querying associations between drug sensitivity and RNA molecules including mRNAs, lncRNAs and miRNAs at four molecular levels (expression, copy number variation, mutation and methylation) from integrated analysis of three large-scale pharmacogenomic databases (GDSC, CellMiner and CCLE). Currently, RNAactDrug contains more than 4924200 RNA molecules-drug sensitivity associations at multidimensional molecular levels covering more than 19770 mRNAs, 11119 lncRNAs, 438 miRNAs and 4155 drugs. RNAactDrug aims to help make use of the full breadth and depth of existing large-scale pharmacogenomic data by making this knowledge accessible to both basic researchers
feature list: operation_0224
feature list: operation 3792

RNAct
type: SoftwareApplication
input: Ensembl transcript ID
  type: FormalParameter
  additional type: data 2725
input: UniProt accession
  type: FormalParameter
  additional type: data 3021
input: Gene symbol
  type: FormalParameter
  additional type: data 1026
input: Ensembl gene ID
  type: FormalParameter
  additional type: data 1033
output: Score
  type: FormalParameter
  additional type: data 1772
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0099
application sub category: topic_0128
application sub category: topic_0602
author: http://orcid.org/0000-0001-6358-8380
citation: gky967
citation: pmcid:PMC6324028
citation: pubmed:30445601
contributor: https://orcid.org/0000-0003-0607-5663
description: Protein–RNA interaction predictions for model organisms with supporting experimental data, enabling a global view of the protein–RNA interactome. RNAct currently covers the human, mouse and yeast genomes and contains a total of 5.87 billion pairwise interactions, reflecting nearly 120 years of computation time on the CRG's high-performance computing cluster. It combines experimentally identified interactions (e.g. from ENCODE) with ab initio predictions, enabling full coverage of the RNA-binding proteome.
feature list: operation 2422
is accessible for free: true
license: CC-BY-NC-SA-4.0
software help: about
primary contact: https://orcid.org/0000-0001-7524-6310

RNAdemocracy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0099
citation: J.COMPBIOLCHEM.2019.107151
citation: pubmed:31751879
description: RNAdemocracy is an ensemble method for RNA secondary structure prediction using consensus scoring.
feature list: operation_0278
feature list: operation_0502
feature list: operation 2441

RNAdt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0097
application sub category: topic_0099
application sub category: topic_0632
application sub category: topic 3168
application sub category: topic 3308
citation: J.BIOSYSTEMS.2019.104065
citation: pubmed:31669269
description: An online tutorial and data portal for the RNA structurome era. This is an animated dialog which is useful for displaying. Timeline of HTS-associated RNA structure probing methods
feature list: operation_0295
feature list: operation_0502
feature list: operation 2441

RNAfamProb Plus NeoFold
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0659
application sub category: topic 3372
citation: https://doi.org/10.1101/812891
description: RNAfamProb Program, Program for Estimations of Posterior Probabilities on RNA Structural alignment. NeoFold Program, Program for Maximum-expected-accuracy Estimations of RNA Secondary Structures with Incorporating Homologous-RNA sequences. This project provides the RNAfamProb program, a program for estimations of posterior probabilities on RNA structural alignment. This project provides the NeoFold Program, a program for the maximum-expected-accuracy estimations of RNA secondary structures with incorporating homologous-RNA sequences. This project has been written in mainly Rust, a systems programming language.
feature list: operation_0278
feature list: operation_0295
feature list: operation_0502

RNAm5CPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0099
application sub category: topic 3170
application sub category: topic 3308
citation: J.OMTN.2019.10.008
citation: pmcid:PMC6859278
citation: pubmed:31726390
description: Prediction of RNA 5-Methylcytosine Sites Based on Three Different Kinds of Nucleotide Composition. RNAm5CPred: A webserver for RNA 5-methylcytosine sites prediction. A webserver for RNA 5-methylcytosine sites prediction. RNAm5CPred was developed by using support vector machine based on three different kinds of nucleotide composition features including KNF (K-nucleotide frequencies), KSNPF (K-spaced nucleotide pair frequencies) and pseDNC (pseudo dinucleotide composition). The input for the server is the RNA sequence. More details can be found in the tutorial
feature list: operation_0224
feature list: operation_0526

RNAsamba
type: SoftwareApplication
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1929
output: Sequence property
  type: FormalParameter
  additional type: data 1254
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0080
application sub category: topic_0659
application sub category: topic 3308
application sub category: topic 3391
application sub category: topic 3474
citation: lqz024
citation: pmcid:PMC7671399
citation: pubmed:33575571
description: RNAsamba is a tool for computing the coding potential of RNA sequences using a neural network classification model. It can be used to identify mRNAs and lncRNAs without relying on database searches.
feature list: operation 2995
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: RNAsamba
software version: 0.2.4

RNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0820
application sub category: topic 3474
citation: J.COMPBIOLCHEM.2019.107094
citation: pubmed:31472418
description: Efficient utilization on PSSM combining with recurrent neural network for membrane protein types prediction | RNN-for-membrane-protein-types-prediction | This repo includes the implementation of preprocessing for proteins and network architecture for training
feature list: operation 2474
feature list: operation 2475
feature list: operation 3439

RNSCLC-PRSP software
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 3421
citation: S13040-019-0205-0
citation: pmcid:PMC6708148
citation: pubmed:31462928
description: RNSCLC-PRSP software to predict the prognostic risk and survival in patients with resected T1-3N0-2 M0 non-small cell lung cancer | Background:The clinical outcomes of patients with resected T1-3N0-2M0 non-small cell lung cancer (NSCLC) with the same tumor-node-metastasis (TNM) stage are diverse. Although other prognostic factors and prognostic prediction tools have been reported in many published studies, a convenient, accurate and specific prognostic prediction software for clinicians has not been developed. The purpose of our research was to develop this type of software that can analyze subdivided T and N staging and additional factors to predict prognostic risk and the corresponding mean and median survival time and 1-5-year survival rates of patients with resected T1-3N0-2M0 NSCLC. Results:Using a Cox proportional hazard regression model, we determined the independent prognostic factors and obtained a prognostic index (PI) eq

ROADMAP epigenomics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2815
application sub category: topic 3173
citation: nature14248
citation: pmcid:PMC4530010
citation: pubmed:25693563
description: Data repository of NIH Roadmap Epigenomics Mapping Consortium containing genome-wide maps of histone modifications, chromatin accessibility, DNA methylation and mRNA expression across 100s of human cell types and tissues.
feature list: operation_0224
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.html
primary contact: Jin Wook Lee

ROBOKOP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0218
application sub category: topic 3855
citation: BTZ604
citation: pubmed:31410449
description: An Abstraction Layer and User Interface for Knowledge Graphs to Support Question Answering | ROBOKOP is a tool for reasoning over structured biomedical knowledge databases as part of the NCATS translator and reasoner programs. The ROBOKOP system consists of a web based user interface, an API server, and several worker servers. The code is separated into three separate repositories
feature list: operation_0224
license: MIT

ROBOKOP KG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3382
citation: ACS.JCIM.9B00683
citation: pubmed:31769676
description: ROBOKOP KG is an Integrated Knowledge Graphs from Federated Sources.
feature list: operation_0224

ROBOT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0769
application sub category: topic 3372
citation: S12859-019-3002-3
citation: pmcid:PMC6664714
citation: pubmed:31357927
description: A Tool for Automating Ontology Workflows | ROBOT is a tool for working with Open Biomedical Ontologies | R.C. Jackson, J.P. Balhoff, E. Douglass, N.L. Harris, C.J. Mungall, and J.A. Overton. ROBOT: A tool for automating ontology workflows. BMC Bioinformatics, vol. 20, July 2019 | ROBOT is a tool for working with Open Biomedical Ontologies. It can be used as a command-line tool or as a library for any language on the Java Virtual Machine | If no --reasoner is provided, ROBOT will default to ELK. The following other reasoner options are supported: | ROBOT will always perform a logical validation check prior to automatic classification | Equivalent Classes (--equivalent-classes-allowed) | Generated Axioms(--axiom-generators)
feature list: operation 2428
feature list: operation 3280
feature list: operation 3559
license: BSD-3-Clause

ROHan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3056
citation: genetics.119.302057
citation: pmcid:PMC6614887
citation: pubmed:31088861
description: Joint inference of Runs of Homozygosity and rates of heterozygosity
operating system: Linux

ROIMCR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0153
application sub category: topic 3172
application sub category: topic 3360
citation: s12859-019-2848-8
citation: pmcid:PMC6525397
citation: pubmed:31101001
description: Powerful analysis strategy for LC-MS metabolomic datasets.
feature list: operation 3628
feature list: operation 3798
is accessible for free: true
license: Unlicense
operating system: Linux
software help: v1
primary contact: Romà Tauler

ROMOP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0621
application sub category: topic 3063
application sub category: topic 3303
application sub category: topic 3489
citation: OOY059
citation: pmcid:PMC6800657
citation: pubmed:31633087
description: a light-weight R package for interfacing with OMOP-formatted electronic health record data. R package to easily interface with OMOP-formatted EHR data. ROMOP, please wait... This may take a minute or two. Launching ROMOP, please wait... This may take a minute or two. ... ROMOP is a flexible R package to interface with the Observational Health Data Sciences and Informatics (OHDSI) OMOP Common Data Model. Briefly, OMOP is a standardized relational database schema for Electronic Health Record (EHR) or Electronic Medical Record (EMR) data (i.e., patient data collected during clinical visits to a health system). The main benefit of a standardized schema is that it allows for interoperability between institutions, even if the underlying EHR vendors are disparate. Benjamin S. Glicksberg 9/14/2018
feature list: operation 2421
feature list: operation 2422
feature list: operation 3435
license: MIT

RPANDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0194
application sub category: topic_0625
application sub category: topic 3293
citation: SYZ057
citation: pubmed:31682272
description: RPAND is an R package for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade–clade competitive effects or the effect of species richness on phenotypic divergence.
feature list: operation_0399
feature list: operation 3745

RPGeNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 2229
application sub category: topic 3518
citation: BAZ120
citation: pmcid:PMC6846243
citation: pubmed:31712826
description: RPGeNet v2.0 - Retinitis Pigmentosa Gene Network: interacting with the network of genes related to retinitis pigmentosa genes.
feature list: operation_0224
feature list: operation 3083
feature list: operation 3439
software version: 2.0

RPITER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0082
application sub category: topic_0602
application sub category: topic_0659
citation: ijms20051070
citation: pmcid:PMC6429152
citation: pubmed:30832218
description: Hierarchical deep learning model for predicting ncRNA-protein interaction.
feature list: operation_0267
feature list: operation_0278
feature list: operation 2495
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md
primary contact: C. Peng

RR-APET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3068
citation: J.CMPB.2019.105127
citation: pubmed:31648100
description: Heart rate variability analysis software. BACKGROUND AND OBJECTIVES:Heart rate variability (HRV) has increasingly been linked to medical phenomena and several HRV metrics have been found to be good indicators of patient health. This has enabled generalised treatment plans to be developed in order to respond to subtle personal differences that are reflected in HRV metrics. There are several established HRV analysis platforms and methods available within the literature; some of which provide command line operation across databases but do not offer extensive graphical user interface (GUI) and editing functionality, while others offer extensive ECG editing but are not feasible over large datasets without considerable manual effort
feature list: operation 3096
feature list: operation 3799

RRBSsim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3295
application sub category: topic 3674
citation: bty174
citation: pubmed:29579198
description: Reduced representation bisulfite sequencing simulator for next-generation sequencing.
feature list: operation_0430
feature list: operation 3186
feature list: operation 3206
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Xiwei Sun

RRDistMaps
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic_0154
application sub category: topic_0176
citation: btu841
citation: pmcid:PMC4410660
citation: pubmed:25540183
description: UCSF Chimera tool for viewing and comparing protein distance maps.
feature list: operation 2937
feature list: operation 2950
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: rrdistmaps.html
primary contact: Conrad C. Huang

RRMdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0108
application sub category: topic_0623
application sub category: topic_0736
citation: bay148
citation: pmcid:PMC6334006
citation: pubmed:30649297
description: Evolutionary-oriented database of RNA recognition motif sequences.
feature list: operation_0239
feature list: operation_0246
feature list: operation_0303
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: S. Dunin-Horkawicz

RRphylo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0625
application sub category: topic 3500
citation: JOURNAL.PONE.0226949
citation: pmcid:PMC6934287
citation: pubmed:31881075
description: A new, fast method to search for morphological convergence with shape data. The goal of RRphylo is to compute phenotypic evolutionary rates, estimate ancestral states, locate rate shifts on the tree, and compare vectors of phenotypes and evolutionary rates among species. RRphylo is not based on any evolutionary model, and is best suited to work with phylogenies of fossil species.
feature list: operation_0323
feature list: operation_0326
feature list: operation_0551

RSAT position-analysis
type: SoftwareApplication
input: Sequence set (nucleic acid)
  type: FormalParameter
  additional type: data 1234
  encoding format: format 1929
output: Sequence motif (nucleic acid)
  type: FormalParameter
  additional type: data 2070
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
additional type: Web service
application sub category: topic_0204
application sub category: topic_0749
application sub category: topic 3511
author: https://orcid.org/0000-0002-8799-8584
citation: https://doi.org/10.1093/nar/28.4.1000
citation: pmcid:PMC102588
citation: pubmed:10648794
description: Detect oligomers (k-mers) whose positional distribution significantly discard from a homogeneous distribution.
feature list: operation_0238
feature list: operation 3472
is accessible for free: true
license: AFL-3.0
operating system: Linux
operating system: Mac
provider: https://orcid.org/0000-0002-8799-8584
software help: http://pedagogix-tagc.univ-mrs.fr/rsat/htmllink.cgi
software help: help.position-analysis.html
software help: installing-RSAT
software help: using-RSAT
software help: tut position-analysis.html
primary contact: https://orcid.org/0000-0002-8799-8584

RSAT - Retrieve Sequence
type: SoftwareApplication
input: Gene ID
  type: FormalParameter
  additional type: data 2295
  encoding format: format 2330
output: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
  encoding format: format 1942
  encoding format: format 1957
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web API
additional type: Web application
additional type: Web service
application sub category: topic_0204
author: https://orcid.org/0000-0002-8799-8584
citation: gky317
citation: pmcid:PMC6030903
citation: pubmed:10641039
citation: pubmed:29722874
description: Starting from a list of genes, returns upstream or downstream sequences.
feature list: operation 2422
is accessible for free: true
operating system: Linux
operating system: Mac
primary contact: https://orcid.org/0000-0002-8799-8584

RSAT Var-tools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
additional type: Web application
application sub category: topic_0749
application sub category: topic 3500
application sub category: topic 3517
citation: https://doi.org/10.1101/623090
description: Accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding.
feature list: operation_0239
feature list: operation_0438
feature list: operation 3197
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Alejandra Medina-Rivera
primary contact: Jacques van Helden

RSAT dyad-analysis
type: SoftwareApplication
input: Sequence set (nucleic acid)
  type: FormalParameter
  additional type: data 1234
  encoding format: format 1929
output: Sequence motif (nucleic acid)
  type: FormalParameter
  additional type: data 2070
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
additional type: Web service
application sub category: topic_0204
application sub category: topic_0749
application sub category: topic 3511
author: https://orcid.org/0000-0002-8799-8584
citation: https://doi.org/10.1093/nar/28.8.1808
citation: pmcid:PMC102821
citation: pubmed:10734201
description: Detect over- or under-represented dyads (spaced pairs of k-mers) in sequences.
feature list: operation_0238
feature list: operation 3472
is accessible for free: true
license: AFL-3.0
operating system: Linux
operating system: Mac
provider: https://orcid.org/0000-0002-8799-8584
software help: http://pedagogix-tagc.univ-mrs.fr/rsat/htmllink.cgi
software help: help.dyad-analysis.html
software help: installing-RSAT
software help: using-RSAT
software help: tut dyad-analysis.html
primary contact: https://orcid.org/0000-0002-8799-8584

RSI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic 3398
citation: gkz417
citation: pmcid:PMC6698671
citation: pubmed:31114928
description: Regulostat Inferelator (RSI) - network biology platform to uncover molecular devices that predetermine cellular response phenotypes.
feature list: operation_0337
feature list: operation 2436
feature list: operation 3463
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: rsi.hulilab.org
primary contact: Hu Li

RSMLM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0632
application sub category: topic 3047
application sub category: topic 3382
citation: btz788
citation: pmcid:PMC7162425
citation: pubmed:31626286
description: Topological data analysis quantifies biological nano-structure from single molecule localization microscopy.
feature list: operation_0337
feature list: operation 3432
license: GPL-3.0
software help: RSMLM-tutorials

RSQLite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3360
application sub category: topic 3512
citation: OL.2019.10733
citation: pmcid:PMC6732981
citation: pubmed:31516576
description: Bioinformatics and functional analyses of key genes in smoking-associated lung adenocarcinoma | Embeds the 'SQLite' database engine in R and provides an interface compliant with the 'DBI' package. The source for the 'SQLite' engine is included
feature list: operation 2495
feature list: operation 3501
feature list: operation 3659
license: LGPL-2.0

RT networks
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3173
citation: GR.247049.118
citation: pmcid:PMC6724675
citation: pubmed:31434679
description: > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'RT', 'TRNs', 'TRNs RT', 'provocative' | Replication timing networks reveal a link between transcription regulatory circuits and replication timing control | Create community RT network For RT Networks visualization. It will return None, but creates txt file for the input for the SAFE algorithm | > pip install -r requirements.txt | Before running below do_something.py, please edit parameters in each file
feature list: operation_0277
feature list: operation_0443
feature list: operation 3439

RUFUS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0749
application sub category: topic_0798
application sub category: topic 3673
citation: GR.247965.118
citation: pmcid:PMC6771411
citation: pubmed:31575651
description: RUFUS is a Pedigree-based estimation of human mobile element retrotransposition rates.

RUV-III
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 3512
application sub category: topic 3518
citation: GKZ433
citation: pmcid:PMC6614807
citation: pubmed:31114909
description: Removing Unwanted Variation-III (RUV-III) - normalization for Nanostring nCounter gene expression data.
feature list: operation 2939
feature list: operation 2940
feature list: operation 3891
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ruv.pdf
primary contact: https://orcid.org/0000-0002-5403-7998
primary contact: Johann Gagnon-Bartsch

RXN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 2258
application sub category: topic 3314
application sub category: topic 3474
citation: CHEMRXIV.9992489.V1
description: RXN is a unique tool for digital chemistry, based on the Molecular Transformer, using a simple Ketcher drawing interface and made it available on IBM Cloud to perform a variety of tasks: converting Experimental Protocols into Action Sequences, predicting Chemical Reactions, Retrosynthesis Pathways, Experimental Procedures and automating the compilation and execution of Chemical Syntheses.
feature list: operation_0337
feature list: operation 3439
feature list: operation 3454

R plus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Software provides direct mapping refence between expanded molecular alphabet and N-nary digits in the absence of high-performance transcoding algorithm at present. Transcoding scheme for DNA data storage based on expanded molecular alphabet.
software help: DNA-storage-R plus

Rqtl2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0160
application sub category: topic_0625
application sub category: topic_0780
citation: genetics.118.301595
citation: pmcid:PMC6366910
citation: pubmed:30591514
description: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations.
feature list: operation_0282
feature list: operation 3196
feature list: operation 3232
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: rqtl.org
software help: qtl2
primary contact: Karl Broman

RaGOO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0780
application sub category: topic 2229
application sub category: topic 3168
citation: S13059-019-1829-6
citation: pmcid:PMC6816165
citation: pubmed:31661016
description: fast and accurate reference-guided scaffolding of draft genomes. Fast Reference-Guided Scaffolding of Genome Assembly Contigs. Index of /shares/schatzlab/www-data/ragoo. A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome. Alonge, Michael, et al. "RaGOO: fast and accurate reference-guided scaffolding of draft genomes." Genome biology 20.1 (2019): 1-17. Contigs and reference fasta files may now be gzipped. RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:
feature list: operation_0525
feature list: operation 3182
feature list: operation 3192
feature list: operation 3216
license: MIT

RaNA-Seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0203
application sub category: topic_0769
application sub category: topic 3170
citation: BTZ854
citation: pubmed:31730197
description: RaNA-Seq is an open bioinformatics tool for the quick analysis of RNA-Seq data. It performs a full analysis in minutes quantifying FASTQ files, calculating quality control metrics, running differential expression analyses and enabling the interpretation of results with functional analyses. Our analysis pipeline integrates cutting edge bioinformatics tools and simplify its application with a friendly Web interface designed for non-experienced users in these analyses. Each analysis can be customized setting up input parameters and applies generally accepted and reproducible protocols. Analysis results are presented as interactive graphics and reports, ready for their interpretation and publication.
feature list: operation 2436
feature list: operation 3680
feature list: operation 3800

Racon
type: SoftwareApplication
input: Sequence set (nucleic acid)
  type: FormalParameter
  additional type: data 1234
  encoding format: format 1930
input: Nucleic acid sequence alignment
  type: FormalParameter
  additional type: data 1383
  encoding format: format 2572
  encoding format: format 2573
input: Sequence set (nucleic acid)
  type: FormalParameter
  additional type: data 1234
  encoding format: format 1929
output: Sequence set (nucleic acid)
  type: FormalParameter
  additional type: data 1234
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic 3673
citation: plants8080270
citation: pmcid:PMC6724115
citation: pubmed:31390788
description: Consensus module for raw de novo DNA assembly of long uncorrected reads Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.
feature list: operation_0523
feature list: operation_0525
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac

RadAA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0196
application sub category: topic 3500
citation: minf.201800057
citation: pmcid:PMC6585820
citation: pubmed:30019526
description: Identification of radical amino acid changes in multiple sequence alignments.
feature list: operation_0292
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Inge Seim

Ragp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 3474
application sub category: topic 3510
citation: CWZ072
citation: pubmed:31508799
description: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R | Filter plant hydroxyproline rich glycoproteins | ragp - hydroxyproline aware filtering of hydroxyproline rich glycoprotein sequences | ragp is an R package primarily designed for mining and analysis of plant hydroxyproline rich glycoproteins. It incorporates a novel concept with an additional analysis layer where the probability of proline hydroxylation is estimated by a machine learning model. Only proteins predicted to contain hydroxyprolines are further analysed for HRGP characteristic motifs and features. ragp can also be used for protein annotation by obtaining predictions for several protein features based on sequence (secretory signals, transmembrane regions, domains, glycosylphosphatidylinositol attachment sites and disordered regions). Additionally ragp provides tools for visualization of the mentioned attributes
feature list: operation_0417
feature list: operation_0418
feature list: operation 3501
license: MIT

RainBio
type: SoftwareApplication
input: Sequence set
  type: FormalParameter
  additional type: data_0850
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0092
application sub category: topic 2269
application sub category: topic 3056
citation: TVCG.2019.2921544
citation: pubmed:31180862
description: RainBio is a visual tool for comparing gene sets or protein sets, in a proportional way. RainBio is an alternative to the classical Venn diagrams and Euler diagrams. In particular, RainBio can compare up to 15 sets, while Venn diagrams are limited to 6, and proportional Venn diagram are approximated above 4 sets. RainBio can perform the exact proportional visualization of up to 6 sets, and support intersection clustering, allowing to visualize up to 15 sets. RainBio uses the same file format that InteractiVenn. Several demo datasets are available on the website.
feature list: operation 3209
feature list: operation 3744
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: 0000-0002-5477-180X

Ramedis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0625
application sub category: topic 3325
application sub category: topic 3407
citation: pubmed:12542423
description: Rare Metabolic Diseases Database: platform independent, web-based information system for rare metabolic diseases based on filed case reports.
feature list: operation 3196
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Thoralf Töpel

RametrixTM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3277
application sub category: topic 3360
application sub category: topic 3422
citation: JOURNAL.PONE.0222115
citation: pmcid:PMC6764656
citation: pubmed:31560690
description: Spectral characteristics of urine specimens from healthy human volunteers analyzed using Raman chemometric urinalysis (Rametrix) | Raman chemometric urinalysis (Rametrix™) was used to analyze 235 urine specimens from healthy individuals. The purpose of this study was to establish the "range of normal" for Raman spectra of urine specimens from healthy individuals. Ultimately, spectra falling outside of this range will be correlated with kidney and urinary tract disease. Rametrix™ analysis includes direct comparisons of Raman spectra but also principal component analysis (PCA), discriminant analysis of principal components (DAPC) models, multivariate statistics, and it is available through GitHub as the Rametrix™ LITE Toolbox for MATLAB®. Results showed consistently overlapping Raman spectra of urine specimens with significantly larger variances in Raman shifts, found by PCA, corresponding to urea, creatinine, and glucose concentrations
feature list: operation 2939
feature list: operation 3891

Ramf
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0780
application sub category: topic 2269
citation: FPLS.2019.01184
citation: pmcid:PMC6777641
citation: pubmed:31611898
description: An Open-Source R Package for Statistical Analysis and Display of Quantitative Root Colonization by Arbuscular Mycorrhiza Fungi. A package for arbuscular mycorrhyzal fungi colonization. Marco Chiapello , Debatosh Das, Caroline Gutjahr. Ramf: An open-source R package for statistical analysis and display of quantitative root colonization by arbuscular mycorrhiza fungi. _Frontiers Plant Science_. **In press**. If you use the package, please cite it:
feature list: operation_0337
feature list: operation 3435
feature list: operation 3799

Ramid
type: SoftwareApplication
input: Mass spectrum
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3650
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 2330
output: Mass spectrum
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3835
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3172
application sub category: topic 3955
citation: 978-1-0716-0159-4 12
citation: pubmed:31893378
description: R-program supporting the initial step of the workflow of 13C assisted fluxomic analysis: extraction of mass spectra (MS) of 13C-labeled metabolites of interest from raw mass spectrometer recordings saved in NetCDF files.
feature list: operation 2409
license: Freeware
operating system: Linux
software help: ramidcor
software version: 0.0.1.0

RankerGUI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0769
application sub category: topic 2830
application sub category: topic 3170
application sub category: topic 3518
citation: IJMS20236098
citation: pmcid:PMC6929103
citation: pubmed:31816915
description: A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics. RankerGUI platform for the comparison of differential expression profiles using a rank-based statistical approach. RankerGUI automates the analysis of complex gene expression signatures. The Pipeline is easy to use and freely available to the scientific community. Users can upload data via a web page and can be notified of the analysis completion by email. The output includes detailed data analysis reports and diagrams. Documentation provides full information on used methods
feature list: operation_0315
feature list: operation_0571
feature list: operation 2436
feature list: operation 3223
feature list: operation 3802

RapidACi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 2269
application sub category: topic 3298
citation: FPLS.2019.01276
citation: pmcid:PMC6823239
citation: pubmed:31708940
description: Measuring Rapid A-Ci Curves in Boreal Conifers. R scripts for automatic correction of Rapid A-Ci curves. An R package for the batch treatment of Rapid carbon dioxide response curves (A-Ci) generated by the LI-COR® portable photosynthesis systems. The Rapid A-Ci measurement method (RACiR™) can save a lot of time characterising photosynthetic capacity of multiple plants. devtools::install_github("ManuelLamothe/RapidACi"). If, later on, you need to adjust leaf area values, you need to provide a dataframe containing at least one column for the unique sample identifier (named: “sample_ID”), and one column with the leaf area in mm2 (named: “LeafArea_mm2”)
feature list: operation 3196
feature list: operation 3435

RaptorX-ComplexContact
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0128
application sub category: topic 2275
application sub category: topic 3474
citation: 978-1-4939-9873-9 6
citation: pubmed:31583631
description: A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning.
feature list: operation_0272
feature list: operation 2492
feature list: operation 3439
feature list: operation 3899

RareLSD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0821
application sub category: topic 2885
application sub category: topic 3172
application sub category: topic 3325
citation: baz112
citation: pmcid:PMC6830269
citation: pubmed:31688938
description: a manually curated database of lysosomal enzymes associated with rare diseases. RareLSD: Database for Human Lysosomal Enzymes. RareLSD: A Database for Human Lysosomal Enzymes. RareLSD is a manually curated database of 63 lysosomal enzymes present in the humans. Deficiency or malfunctioning of any enzyme leads to accumulation of toxic metabolites and thus, various storage defects. One major application of this database is, all the necessary information about these enzymes can be found in this portal
feature list: operation_0495
feature list: operation 2421
feature list: operation 2422

RatMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: RatMine integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. You can run flexible queries, export results and analyse lists of data. The Rat Genome Database (RGD) was established in 1999 and is the premier site for genetic, genomic, phenotype, and disease data generated from rat research. In addition, it provides easy access to corresponding human and mouse data for cross-species comparisons. RGD's comprehensive data and innovative software tools make it a valuable resource for researchers worldwide.
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest

Ratcave
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3382
citation: s13428-019-01245-x
citation: pmcid:PMC6797704
citation: pubmed:31062192
description: 3D graphics python package for cognitive psychology experiments.
feature list: operation_0337
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: ratcave.readthedocs.io
primary contact: Del Grosso NA

Ravages
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 3676
citation: GEPI.22210
citation: pubmed:31087445
description: Rare variant association testing for multicategory phenotype.
feature list: operation 3196
feature list: operation 3659
feature list: operation 3791
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Hervé Perdry

RaxmlGUI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0769
application sub category: topic 3293
citation: https://doi.org/10.1101/800912
description: raxmlGUI1,2 is a graphical user interface to RAxML3, one of the most popular and widely used software for phylogenetic inference using maximum likelihood.
software version: 2.0

Rbbt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0769
application sub category: topic 3168
application sub category: topic 3382
application sub category: topic 3577
citation: JOURNAL.PCBI.1007291
citation: pmcid:PMC6797086
citation: pubmed:31622330
description: Rbbt stands for “Ruby Bioinformatics Toolkit”. It is a framework for software development in bioinformatics. It covers three aspects:. Workflow wrapping the TF text-mining results from https://github.com/fnl plus other databases. High Throughput Sequencing related functionalities. Rbbt wrapper for the Variant Effect Predictor. Auto-downloads and installs the software.
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feature list: operation_0337
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feature list: operation 3501
feature list: operation 3802

Rchimerism
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
application sub category: topic 3421
application sub category: topic 3520
citation: J.JMOLDX.2019.08.005
citation: pubmed:31605803
description: An R Package for Automated Chimerism Data Analysis.
feature list: operation 3799

ReCirc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0632
application sub category: topic 3512
application sub category: topic 3518
citation: c8mo00252e
citation: pubmed:30916068
description: Prediction of circRNA expression and function through probe reannotation of non-circRNA microarrays.
feature list: operation_0308
feature list: operation_0309
feature list: operation 2495
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: ReCirc

ReDU
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3172
application sub category: topic 3520
citation: https://doi.org/10.1101/750471
description: Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data | User interface to reanalyze and explore all public data in Metabolomics Public Data | Reanalysis of Data User Interface for MS2 (ReDU) | Compare Your Data to Public Data via Multivariate Analysis | ReDU is a community- and data-driven approach to find and reuse public data containing tandem MS data at the repository scale. ReDU is a launchpad for co- or re-analysis of public data via the Global Natural Product Social Molecular Networking Platform (GNPS). Our aim is to empower researchers to put their data in the context of public data as well as explore questions using public data at the repository scale | Reanalysis of Data User Interface | Projection of your data onto a precalculated principal components analysis score plot of public data
feature list: operation 2939
feature list: operation 3501
feature list: operation 3801
license: MIT
software help: ReDU-MS2-Documentation

ReFDash
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: PREPRINTS201909.0070.V1
description: A Repository of Functional Dashboards providing comprehensive functional insights inferred from 16S microbiome data sets | Motivation: 16S rRNA gene amplicon based sequencing has significantly expanded the scope of metagenomics research by enabling microbial community analyses in a cost-effective manner. The possibility to infer functional potential of a microbiome through amplicon sequencing derived taxonomic abundance profiles has further strengthened the utility of 16S sequencing. In fact, a surge in 'inferred function metagenomic analysis' has recently taken place, wherein most 16S microbiome studies include inferred functional insights in addition to taxonomic characterization. Tools like PICRUSt, Tax4Fun, Vikodak and iVikodak have significantly eased the process of inferring function potential of a microbiome using the taxonomic abundance profile
feature list: operation_0310
feature list: operation_0362
feature list: operation 2495

ReFernment
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0196
application sub category: topic 3170
application sub category: topic 3512
citation: aps3.1216
citation: pmcid:PMC6384294
citation: pubmed:30828503
description: R package for annotating RNA editing in plastid genomes.
feature list: operation_0310
feature list: operation 3096
feature list: operation 3431
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.1.2
primary contact: Tanner Robison

ReGEO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0218
application sub category: topic 3174
application sub category: topic 3518
citation: bay145
citation: pmcid:PMC6333964
citation: pubmed:30649296
description: Restructured version of Gene Expression Omnibus (GEO) that provides a user friendly interface for curating GEO database
feature list: operation_0306
feature list: operation 2422
feature list: operation 2495
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.jsp
primary contact: Canglin Wu

ReMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3169
application sub category: topic 3295
application sub category: topic 3512
citation: gkz945
citation: pmcid:PMC7145625
citation: pubmed:31665499
description: THIS PAGE IS DEPRECATED, GO TO : https://bio.tools/inserm-remap
feature list: operation 2421
feature list: operation 3192
feature list: operation 3208
feature list: operation 3222

ReProMin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0204
application sub category: topic_0602
citation: https://doi.org/10.1101/733592
description: > MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'jats:list-item' | A quantitative method for proteome reallocation using minimal regulatory interventions | Regulation based Proteome Minimization (ReProMin) | Three files are needed for the analysis:
feature list: operation_0277
feature list: operation 1781
feature list: operation 3439

ReQTL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic_0659
application sub category: topic 3170
citation: btz750
citation: pmcid:PMC7058180
citation: pubmed:31589315
description: Identifying correlations between expressed SNVs and gene expression using RNA-sequencing data. This toolkit contains the required scripts to transform sequencing files into ReQTL input files and run the MatrixEQTL R package to identify significant variation-expression relationships
feature list: operation 3196
feature list: operation 3463
feature list: operation 3799

ReSimNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 3336
application sub category: topic 3474
citation: BTZ411
citation: pubmed:31116384
description: Drug response similarity prediction using Siamese neural networks.
feature list: operation 3501
is accessible for free: true
license: Apache-2.0
operating system: Linux
software help: README.md

ReVac
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0121
application sub category: topic_0160
application sub category: topic 2830
application sub category: topic 3474
citation: S12864-019-6195-Y
citation: pmcid:PMC6916091
citation: pubmed:31842745
description: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates. BACKGROUND:Reverse vaccinology accelerates the discovery of potential vaccine candidates (PVCs) prior to experimental validation. Current programs typically use one bacterial proteome to identify PVCs through a filtering architecture using feature prediction programs or a machine learning approach. Filtering approaches may eliminate potential antigens based on limitations in the accuracy of prediction tools used. Machine learning approaches are heavily dependent on the selection of training datasets with experimentally validated antigens (positive control) and non-protective-antigens (negative control). The use of one or few bacterial proteomes does not assess PVC conservation among strains, an important feature of vaccine antigens
feature list: operation_0252
feature list: operation_0416
feature list: operation 2489

ReaDDy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0176
application sub category: topic_0602
application sub category: topic 3314
citation: journal.pcbi.1006830
citation: pmcid:PMC6413953
citation: pubmed:30818351
description: Reaction Diffusion Dynamics (ReaDDy) - software framework for interacting-particle reaction dynamics.
feature list: operation_0334
feature list: operation 2476
feature list: operation 3457
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: readdy.github.io
software help: installation.html
primary contact: ReaDDy

ReactPRED
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 3068
application sub category: topic 3292
citation: btw491
citation: pubmed:27485447
description: Tool to predict and analyze biochemical reactions.
feature list: operation 2497
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: download
primary contact: Anirban Bhaduri
primary contact: Tae Yong Kim

Read-SpaM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0121
application sub category: topic_0194
application sub category: topic_0196
citation: S12859-019-3205-7
citation: pmcid:PMC6916211
citation: pubmed:31842735
description: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage. Read-SpaM. Test runs on simulated reads from bacterial genomes show that our approach can estimate phylogenetic distances with high accuracy, even for large evolutionary
feature list: operation_0289
feature list: operation_0557
feature list: operation 3472
feature list: operation 3478
feature list: operation 3695
license: GPL-3.0

Real-time
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3172
application sub category: topic 3300
application sub category: topic 3390
application sub category: topic 3407
application sub category: topic 3520
citation: S41746-019-0185-Y
citation: pmcid:PMC6848197
citation: pubmed:31728416
description: Real-time is a health monitoring through urine metabolomics.
feature list: operation 2939
feature list: operation 3799
feature list: operation 3803

RealityConvert
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Tool for preparing 3D models of biochemical structures for augmented and virtual reality.
primary contact: Denis Fourches

Recentrifuge
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: journal.pcbi.1006967
citation: pmcid:PMC6472834
citation: pubmed:30958827
description: Robust comparative analysis and contamination removal for metagenomics.
feature list: operation 2495
feature list: operation 3460
feature list: operation 3730
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 0.28.10
primary contact: Jose Manuel Martí

Reciprocal Best Hits - Best Bidirectional Hits
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0091
application sub category: topic_0194
application sub category: topic_0797
application sub category: topic 3293
citation: pnas.96.6.2896
citation: journal.pone.0101850
citation: pmcid:PMC15866
citation: pmcid:PMC4094424
citation: pubmed:10077608
citation: pubmed:25013894
description: Reciprocal Best Hits (RBH) are a common proxy for orthology in comparative genomics. Essentially, a RBH is found when the proteins encoded by two genes, each in a different genome, find each other as the best scoring match in the other genome. NCBI's BLAST is the software most usually used for the sequence comparisons necessary to finding RBHs.
feature list: operation_0292
feature list: operation 2423
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
primary contact: 0000-0002-6981-397X

ReferenceSeeker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic 3293
author: http://orcid.org/0000-0003-4216-2721
citation: joss.01994
description: Rapid determination of appropriate reference genomes.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software version: v1.7.3

Reference Panel Reconstruction
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0625
application sub category: topic 3305
application sub category: topic 3517
citation: https://doi.org/10.1101/642546
description: Tool for users to reconstruct imputation reference panels of 1000G, and to investigate the imputation accuracy changes pattern for a particular population of interest.
feature list: operation_0487
feature list: operation 3196
feature list: operation 3557
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

refgenie
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web API
additional type: Web service
application sub category: topic_0080
citation: https://doi.org/10.1101/698704
description: Refgenie manages storage, access, and transfer of reference genome resources. It provides command-line and Python interfaces to download pre-built reference genome "assets", like indexes used by bioinformatics tools. It can also build assets for custom genome assemblies. Refgenie provides programmatic access to a standard genome folder structure, so software can swap from one genome to another.
feature list: operation 2422
is accessible for free: true
license: BSD-2-Clause
operating system: Linux
operating system: Mac

RegLinker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3855
citation: BTZ360
citation: pmcid:PMC6612893
citation: pubmed:31510694
description: Reconstructing signaling pathways using regular language constrained paths | Connect the dots in protein interaction networks ... using regular expressions! | RegLinker is an algorithm for the automated curation of signaling pathways. Given a signaling pathway and a background interactome, RegLinker will automatically rank the interactions in the background interactome as candidates for inclusion into the signaling pathway | Connect the dots in protein interaction networks... using regular expressions!
feature list: operation_0277
feature list: operation 3083
feature list: operation 3439
license: GPL-3.0

RegSNPs-intron
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0166
application sub category: topic_0634
application sub category: topic 2885
application sub category: topic 3320
application sub category: topic 3512
citation: S13059-019-1847-4
citation: pmcid:PMC6883696
citation: pubmed:31779641
description: a computational framework for predicting pathogenic impact of intronic single nucleotide variants. Predict disease-causing probability of human intronic SNVs. regSNP-intron is a tool which predicts disease-causing probability of human intronic single nucleotide variants (iSNVs). regsnp-intron predicts the disease-causing probability of intronic single nucleotide variants (iSNVs) based on both genomic and protein structural features. ANNOVAR (>= 2016Feb01): Follow the instructions at http://annovar.openbioinformatics.org/en/latest to install, and prepare Ensembl gene annotation. Or paste input here (use example). Or upload a file size limit: 10K rows
feature list: operation_0417
feature list: operation 2499
feature list: operation 3461
license: MIT

RegScan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3172
application sub category: topic 3517
citation: bbt066
citation: pmcid:PMC4293375
citation: pubmed:24008273
description: Performance of fast association analysis between allele frequencies and continuous traits. Uses linear regression to estimate marker effects on continuous traits.
feature list: operation 3659
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software version: 0.5
primary contact: T. Haller

RegulationSpotter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3325
citation: gkz327
citation: pmcid:PMC6602480
citation: pubmed:31106382
description: RegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of 'extratranscriptic' DNA variants. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region. Phenotypic data can be used to focus on likely disease genes.
feature list: operation 3225
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

RelocaTE2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0780
application sub category: topic_0798
application sub category: topic 3168
citation: peerj.preprints.2447v2
description: a high resolution transposable element insertion site mapping tool for population resequencing. This tool is for mapping TEs from resequencing data: Stajich lab. RelocaTE2: a high resolution transposable element insertion sites mapping tool for population resequencing. RelocaTE2 is an improved version of RelocaTE (Robb et al., 2013). RelocaTE2 is highly sensitive and accurate in mapping transposable elements (TE) polymorphisms at single base pair resolution. RelocaTE2 uses the reads associated with TEs as seeds to cluster the read pairs on chromosomes. It automatically detects the target site duplication (TSD) of a TE insertion from alignments in each cluster, which enable high resolution mapping of TE polymorphisms. Unlike parallel searching of multi-TE elements in RelocaTE, RelocaTE2 searches all TEs in one cycle, which enables us find polymorphisms of thousands of TEs in an individual genome or large population in a reasonable timeframe without losing sensitivity and specificity
feature list: operation_0452
feature list: operation 3192
feature list: operation 3196
license: MIT

RemeDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0160
application sub category: topic_0821
application sub category: topic 3174
application sub category: topic 3837
citation: CMB.2019.0345
citation: pubmed:31800321
description: Tool for Rapid Prediction of Enzymes Involved in Bioremediation from High-Throughput Metagenome Data Sets. Venue - Responsive HTML5 Template. Tool to identify Bioremediation enzymes from. RemeDB aims at identifying Pollutant Degrading Enzymes (PDE) from metagenomic sequences. A hassle-free tool to predict bioremediation enzymes from metagenomic datasets
feature list: operation_0417
feature list: operation 2421

ReorientExpress
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3474
application sub category: topic 3512
citation: S13059-019-1884-Z
citation: pmcid:PMC6883653
citation: pubmed:31783882
description: reference-free orientation of nanopore cDNA reads with deep learning. Transcriptome long-read orientation with Deep Learning. ReorientExpress is a program to create, test and apply models to predict the 5'-to-3' orientation of long-reads from cDNA sequencing with Nanopore or PacBio using deep neural networks for samples without a genome or a transcriptome reference. For details on the benchmarkings and analyses performed with this program, please see our publication: https://www.ncbi.nlm.nih.gov/pubmed/31783882
feature list: operation 3192
feature list: operation 3198
feature list: operation 3472
license: MIT

RepEx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0157
application sub category: topic 2885
application sub category: topic 3399
citation: j.compbiolchem.2018.12.015
citation: pubmed:30598392
description: Web server to extract sequence repeats from protein and DNA sequences.
feature list: operation_0237
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Professor K. Sekar

RepeatFiller
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0621
application sub category: topic_0749
application sub category: topic_0798
citation: giz132
citation: pmcid:PMC6862929
citation: pubmed:31742600
description: RepeatFiller incorporates newly-detected repeat-overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in the chains, which makes it feasible to consider all seeds including those that overlap repetitive regions.
feature list: operation_0491
feature list: operation_0495
feature list: operation 3182

RepeatModeler2
type: SoftwareApplication
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0157
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic_0798
application sub category: topic 3673
citation: https://doi.org/10.1101/856591
description: RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.
feature list: operation_0362
feature list: operation_0525
feature list: operation 3644
is accessible for free: true
license: OSL-2.0
operating system: Linux
operating system: Mac
software version: 2.0.7

RepeatScout
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0654
citation: bti1018
citation: pubmed:15961478
description: RepeatScout is a tool to discover repetitive substrings in DNA.
feature list: operation 3472

RepetDB
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: Repeats intermine database
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 1

Res2Net
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3382
application sub category: topic 3474
citation: TPAMI.2019.2938758
citation: pubmed:31484108
description: A New Multi-scale Backbone Architecture | A New Multi-scale Backbone Architecture – 程明明教授主页 | Figure 1. We propose a novel building block for CNNs, namely Res2Net, by constructing hierarchical residual-like connections within one single residual block. The Res2Net represents multi-scale features at a granular level and increases the range of receptive fields for each network layer. The proposed Res2Net block can be plugged into the state-of-the-art backbone CNN models, e.g., ResNet, ResNeXt, BigLittleNet, and DLA. We evaluate the Res2Net block on all these models and demonstrate consistent performance gains over baseline models
feature list: operation_0479
feature list: operation 3436

ResDisMapper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0621
application sub category: topic 3053
citation: https://doi.org/10.1111/1755-0998.13127
citation: pubmed:31845517
description: An R package for fine-scale mapping of resistance to dispersal. Management of biological invasions and conservation activity in the fight against habitat fragmentation both require information on how ongoing dispersal of organisms is affected by the environment. However, there are few landscape genetic programs that map resistance to dispersal at small spatiotemporal scales. To facilitate such analyses, we present an R package named ResDisMapper for the mapping of resistance to dispersal at small spatiotemporal scales, without the need for prior knowledge on environmental features or intensive computation. Based on the concept of isolation by distance (IBD), ResDisMapper calculates resistance using deviations of each pair of samples from the general IBD trend (IBD residuals). The IBD residuals are projected onto the studied area, which allows construction and visualization of a fine-scale map of resistance based on spatial accumulation of positive or negative IBD residuals
feature list: operation_0282
feature list: operation 2950

ResPRE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0108
application sub category: topic_0602
application sub category: topic 3474
citation: btz291
citation: pmcid:PMC6853658
citation: pubmed:31070716
description: Algorithm for protein residue-residue contact-map prediction.
feature list: operation_0267
feature list: operation_0272
feature list: operation_0303
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Yang Li

ResidueDisorder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0130
application sub category: topic_0736
application sub category: topic 3538
citation: ACS.JPCB.9B04333
citation: pmcid:PMC6748046
citation: pubmed:31411026
description: Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder | Many proteins contain regions of intrinsic disorder, not folding into unique, stable conformations. Numerous experimental methods have been developed to measure the disorder of all or select residues. In the absence of experimental data, computational methods are often utilized to identify these disordered regions and thus gain a better understanding of both structure and function. Many freely available computational methods have been developed to predict regions of intrinsic disorder from the primary sequence of a protein, including our recently developed Rosetta ResidueDisorder. While these methods are very useful, they are only designed to predict intrinsic disorder from the sequence
feature list: operation_0244
feature list: operation_0303
feature list: operation 3904

RestraintLib
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0077
application sub category: topic_0078
application sub category: topic_0081
citation: gkz1122
citation: pmcid:PMC6954431
citation: pubmed:31799624
description: Programs can use RestraintLib's API to calculate restraints programmatically without interacting with this web page. To see the format of the requests, check the API documentation.
feature list: operation_0249
feature list: operation 1844
feature list: operation 2518

RetSynth
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3398
application sub category: topic 3407
citation: S12859-019-3025-9
citation: pmcid:PMC6734243
citation: pubmed:31500573
description: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms | The overaching goal of RetSynth is to streamline the arduous and complex step of selecting enzyme/reactions pairs to produce a target compound for bioengineering microbial organisms
feature list: operation 3083
feature list: operation 3439
feature list: operation 3660
license: BSD-2-Clause

Rhapsody
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0154
application sub category: topic_0749
citation: https://doi.org/10.1101/737429
description: Pathogenicity prediction of human missense variants based on protein sequence, structure and dynamics | computationally predicting effects of saturation mutagenesis | In silico saturation mutagenesis | perform a complete scan of all possible 19 amino acid substitutions at each site on a human sequence. See example: H-Ras
feature list: operation_0331
feature list: operation_0477
feature list: operation 3461

RiboFlow
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic 2229
citation: https://doi.org/10.1101/855445
description: RiboFlow is an ecosystem for analyzing ribosome profiling data at read length resolution.
feature list: operation_0310
feature list: operation 2495
feature list: operation 3436

RiboPy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic 2229
citation: https://doi.org/10.1101/855445
description: RiboPy is an ecosystem for analyzing ribosome profiling data at read length resolution.
feature list: operation_0310
feature list: operation 2495
feature list: operation 3436

RiboR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0659
application sub category: topic_0769
application sub category: topic 2229
application sub category: topic 3170
citation: https://doi.org/10.1101/855445
description: Ribo Ecosystem is a set of software tools, built around the ribo file format, to facilitate analyzing ribosome profiling data at ribosome protected footprint length resolution. It consists of a pipeline, RiboFlow, and two interfaces RiboR and RiboPy.
feature list: operation_0310
feature list: operation 2495
feature list: operation 3436

RiboVIEW
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 2229
application sub category: topic 3512
citation: gkz1074
citation: pmcid:PMC6954398
citation: pubmed:31777932
description: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data. Visualization, Quality and Statistics for Ribosome Profiling. This is package RiboVIEW for Visualization, Quality and Statistics for Ribosome Profiling
feature list: operation_0337
feature list: operation 2428
feature list: operation 2495
feature list: operation 3192
feature list: operation 3891

Ribopeaks
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3474
application sub category: topic 3520
citation: bty215
citation: pubmed:29659702
description: Web tool for bacterial classification through m/z data from ribosomal proteins.
feature list: operation 2929
feature list: operation 3460
feature list: operation 3627
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: ribopeaks manual.pdf
primary contact: Rafael Mazer Etto

RiceRelativesGD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0610
application sub category: topic_0623
application sub category: topic 3293
citation: BAZ110
citation: pmcid:PMC6764101
citation: pubmed:31560050
description: a genomic database of rice relatives for rice research | Welcome to RiceRelativesGD, a genomic database of rice relatives for rice research! | The cultivated rice (Oryza sativa) is one of the most important crops in the world
feature list: operation_0553
feature list: operation 3431
feature list: operation 3501

Rice Galaxy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 3810
citation: GIZ028
citation: pmcid:PMC6527052
citation: pubmed:31107941
description: Open resource for plant science.
feature list: operation_0308
feature list: operation 3196
feature list: operation 3232
is accessible for free: true
license: AFL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: rice-galaxy
primary contact: 0000-0001-8512-144X

Rice Genome Hub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 3321
application sub category: topic 3366
description: An open source database(s) for genetics, genomics and functional research in rice species
feature list: operation_0292
feature list: operation_0337
funder: CRP Rice
is accessible for free: true
operating system: Linux
software help: terms-service
primary contact: https://orcid.org/0000-0001-6934-1215
primary contact: 0000-0001-8153-276X
primary contact: https://orcid.org/0000-0003-1849-1269

RobNorm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic 3172
application sub category: topic 3520
citation: https://doi.org/10.1101/770115
description: > MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | > CORRECT NAME OF TOOL COULD ALSO BE 'PQN', 'Windham', 'eGTEx' | Model-Based Robust Normalization for High-Throughput Proteomics from Mass Spectrometry Platform | Abstract Motivation In the analysis of proteomics data from mass spectrometry (MS), normalization is an important preprocessing step to correct sample-level variation and make abundance measurements for each specific protein comparable across different samples. Under heterogeneous samples such as in the Phase I study of the Enhancing Genotype-Tissue Expression (eGTEx) project (Jiang, et al., 2019), the samples coming from 32 different tissues, and without prior housekeeping protein information or spike-ins, how to robustly correct the bias but keep tissue internal variations becomes a challenging question. Majority of previous normalization methods cannot guarantee a robust and tissue adaptive correction
feature list: operation 3454
feature list: operation 3557
feature list: operation 3639

RocaSec
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0123
application sub category: topic_0736
application sub category: topic_0749
citation: BTZ890
citation: pubmed:31800008
description: A standalone GUI-based package for robust co-evolutionary analysis of proteins. RocaSec is a standalone cross-platform package which features an easy-to-use GUI. The package only requires the multiple sequence alignment data of a protein for inferring the underlying co-evolutionary sectors. In addition, when information on the protein biochemical domains is provided, RocaSec returns the corresponding statistical association between inferred sectors and biochemical domains
feature list: operation 3658
feature list: operation 3767
license: MIT

RBM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3315
application sub category: topic 3382
application sub category: topic 3474
citation: TIP.2019.2946455
citation: pubmed:31634130
description: RBM ( Restricted Boltzmann Machine ) is an unsupervised Rotation Factorization in Restricted Boltzmann Machines.

RsHSF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3519
citation: S12864-019-6121-3
citation: pmcid:PMC6814140
citation: pubmed:31651257
description: Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish.
feature list: operation_0239
feature list: operation 2421
feature list: operation 3216
feature list: operation 3799

RsQTL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3320
application sub category: topic 3512
citation: https://doi.org/10.1101/840504
description: correlation of expressed SNVs with splicing using RNA-sequencing data. RsQTL: correlation of expressed SNVs with splicing patterns using RNA-sequencing data. This toolkit contains the required scripts to transform sequencing files into RsQTL input files and run the MatrixEQTL R package to identify significant variation-splicing relationships
feature list: operation 2939
feature list: operation 3800
feature list: operation 3891

RuleBuilder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 2259
application sub category: topic 3315
citation: 978-1-4939-9102-0 2
citation: pubmed:30945241
description: tool for drawing graphs that can be represented by the BioNetGen language, which is used to formulate mathematical, rule-based models of biochemical systems.
feature list: operation 2426
feature list: operation 3216
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
software help: README.md

RxnSim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0821
application sub category: topic 2258
application sub category: topic 3314
citation: btv416
citation: pubmed:26187943
description: Tool computes reaction similarity based on the molecular signatures of participating molecules.
feature list: operation 2929
feature list: operation 3502
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: RxnSim.pdf
primary contact: Anirban Bhaduri
primary contact: Tae Yong Kim
primary contact: Varun Giri

S-conLSH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3168
application sub category: topic 3314
citation: https://doi.org/10.1101/801118
description: Alignment-free gapped mapping of noisy long reads. Spaced context based Locality Sensitive Hashing. Spaced context based Locality Sensitive Hashing (S-conLSH) is a new mapper that facilitates gapped mapping of noisy long reads to the corresponding target locations of a reference genome, with multiple spaced patterns. Spaced-context based Locality Sensitive Hashing
feature list: operation_0491
feature list: operation 3198
feature list: operation 3211
license: GPL-3.0

S4TE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0749
citation: journal.pcbi.1006847
citation: pmcid:PMC6448907
citation: pubmed:30908487
description: Searching algorithm for Type IV effector proteins (S4TE) - software package developed for the prediction of Type IV effector proteins and the analysis of their genomic context.
feature list: operation_0417
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 2.0

SAAVpedia
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic 3520
citation: ACS.JPROTEOME.9B00366
citation: pubmed:31612721
description: Identification, Functional Annotation, and Retrieval of Single Amino Acid Variants for Proteogenomic Interpretation. SAAVpedia is a platform for identification, functional annotation, retrieval of single amino-acid variants from proteomic and genomic data. Home Y.-M. Kang 2019-12-24T08:52:37+00:00. S ingle A mino- A cid V ariant Encyclo pedia :. User Guide Y.-M. Kang 2018-11-28T11:06:16+00:00. The SAAVpedia is a comprehensive proteogenomic interpretation platform that identifies, annotates, and retrieves SAAVs from proteomic and genomic sequence data to discover true pathogenic variant candidates. SAAVpedia provides a proteogenomic analysis pipeline to prioritize and interpret SAAVs. The SAAVpedia is a platform to identify, annotate, and retrieve pathogenic SAAV candidates from proteomic and genomic data. Identification, functional annotation, and retrieval of single amino-acid variants for proteogenomic interpretation
feature list: operation 2421
feature list: operation 2422
feature list: operation 3226
feature list: operation 3436
license: Apache-2.0
software help: guide

SACMES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0749
application sub category: topic 3370
citation: ACS.ANALCHEM.9B02553
citation: pubmed:31462040
description: Open Source Software for the Real-Time Control, Processing, and Visualization of High-Volume Electrochemical Data | This repository contains the master script for the SACMES program and all updates | All updates for the Standard Operating Procedure (SOP) can be viewed here: https://www.dropbox.com/preview/NetzLab%20SACMES%20SOP/2019_11_13%20SACMES%20SOP.docx?role=personal
feature list: operation_0337
feature list: operation 3216
feature list: operation 3431

SAD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0610
application sub category: topic 3277
citation: PEERJ.PREPRINTS.78V2
description: SAD contains efficient algorithms for sampling feasible sets of abundance distributions.

SAIM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3382
citation: S41598-019-48455-Z
citation: pmcid:PMC6704125
citation: pubmed:31434941
description: High-speed device synchronization in optical microscopy with an open-source hardware control platform | Check out the preprint at https://doi.org/10.1101/533349 for more details | This project has been developed in house by the Paszek and Zipfel labs at Cornell University over a few years and several revisions. The primary developer has been Marshall Colville (mjc449@cornell.edu) with assistance from Warren Zipfel and Matt Paszek | Given the scope of the project, the multiple revisions and adaptations that the hardware and software have gone through, and the fact that we are not electrical or software engineers the code tends to change styles and not follow typical conventions

SALSA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 3125
citation: JOURNAL.PCBI.1007273
citation: pmcid:PMC6719893
citation: pubmed:31433799
description: > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch
feature list: operation_0524
feature list: operation_0525
feature list: operation 3216
license: MIT

SALTClass
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0218
application sub category: topic 3063
application sub category: topic 3335
application sub category: topic 3379
application sub category: topic 3474
citation: https://doi.org/10.1101/801944
description: classifying clinical short notes using background knowledge from unlabeled data. Short and Long Text Classifier using clustering-based enrichment. .. :Travis: image:: https://travis-ci.com/bagheria/saltclass.svg?token=fYbdQUbpnoucyHyb3fs2&branch=master .. _Travis: https://travis-ci.com/bagheria/saltclass. saltclass (Short and Long Text Classifier) is a Python module for text classification built under the MIT license. The project was started in 2018 at the Department of Methodology & Statistics, Utrecht University
feature list: operation 1812
feature list: operation 3432
feature list: operation 3625
license: MIT

SAMDUDE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0622
application sub category: topic 3673
citation: S41598-019-51418-Z
citation: pmcid:PMC6803637
citation: pubmed:31636330
description: Denoising of Aligned Genomic Data. Universal denoiser for genomic sequencing. SAMDUDE is a genomic sequence denoiser that operates on aligned SAM files. It both denoises individual bases in reads as well as updates the corresponding quality scores
feature list: operation 3182
feature list: operation 3198
feature list: operation 3227
feature list: operation 3675
feature list: operation 3802

SAME-clustering
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0099
application sub category: topic 3170
application sub category: topic 3308
citation: gkz959
citation: pmcid:PMC6943136
citation: pubmed:31777938
description: Single-cell Aggregated Clustering via Mixture Model Ensemble. SAME (Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble): Cluster ensemble for single-cell RNA-seq data. SAMEclustering (Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble): Cluster ensemble for single-cell RNA-seq data. Although several methods have been recently developed to cluster single-cell RNA-seq (scRNA-Seq) data, they utilize different characteristics of data and yield varying results in terms of both the number of clusters and actual cluster assignments
feature list: operation 3432
feature list: operation 3435
feature list: operation 3436

SAMIRIX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3384
application sub category: topic 3452
citation: FNEUR.2019.01117
citation: pmcid:PMC6886563
citation: pubmed:31824393
description: SAMIRIX is a custom-developed intraretinal segmentation pipeline. It modularly includes import filters for OCT data, a 3rd-party segmentation algorithm, a user interface for controlling and correcting segmentation results, and batch-operations for processing multiple OCT images.
feature list: operation 3435
license: MIT

SAMMI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3068
application sub category: topic 3407
citation: BTZ927
citation: pubmed:31851289
description: A Semi-Automated Tool for the Visualization of Metabolic Networks. Semi-Automated Metabolic Map Illustrator. SAMMI is a web-based tool for the visualization of metabolic networks and related data. Networks can be uploaded directly from KEGG annotated pathways or using constraint-based metabolic reconstructions
feature list: operation_0573
feature list: operation 1812
feature list: operation 3083
feature list: operation 3660
license: GPL-3.0

SAMbinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
additional type: Web service
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic 3534
citation: https://doi.org/10.1101/625806
description: Web server for predicting SAM binding residues of a protein from its amino acid sequence.
feature list: operation_0272
feature list: operation_0417
feature list: operation 2575
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: help.html
primary contact: G.P.S. Raghava

SAPH-ire TFx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic 3474
citation: https://doi.org/10.1101/731026
description: A Machine Learning Recommendation Method and Webtool for the Prediction of Functional Post-Translational Modifications | ABSTRACT Post-translational Modifications (PTMs), chemical or proteinaceous covalent alterations to the side chains of amino acid residues in proteins, are a rapidly expanding feature class of significant importance in cell biology. Due to a high burden of experimental proof and the lack of effective means for experimentalists to prioritize PTMs by functional significance, currently less than ~2% of all PTMs have an assigned biological function. Here, we describe a new artificial neural network model, SAPH-ire TFx for the functional prediction of experimentally observed eukaryotic PTMs. Unlike previous functional PTM prioritization models, SAPH-ire TFx is optimized with both receiver operating characteristic (ROC) and recall metrics that maximally capture the range of diverse feature sets comprising the functional modified eukaryotic proteome
feature list: operation_0417
feature list: operation_0480
feature list: operation 3755

SASM-VGWAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3360
application sub category: topic 3384
application sub category: topic 3444
citation: btz401
citation: pmcid:PMC6954655
citation: pubmed:31095298
description: Matlab package for incorporating spatial-anatomical similarity into the VGWAS framework to detect significant biomarkers in both genetic and imaging data of neurodegenerative diseases.
feature list: operation 3196
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Meiyan Huang
primary contact: Qianjin Feng

SAUCIE
type: SoftwareApplication
input: Matrix
  type: FormalParameter
  additional type: data 2082
  encoding format: format 3752
output: Matrix
  type: FormalParameter
  additional type: data 2082
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 3474
citation: s41592-019-0576-7
citation: pmcid:PMC10164410
citation: pubmed:31591579
description: SAUCIE is a python object that loads data from a numpy matrix and produces numpy matrix output for the reconstruction, visualization, and/or clusters.
feature list: operation_0337
feature list: operation 3432
feature list: operation 3557
feature list: operation 3664
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

SAVER-X
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3474
citation: s41592-019-0537-1
citation: pmcid:PMC7781045
citation: pubmed:31471617
description: Data denoising with transfer learning in single-cell transcriptomics | R package for transfer learning of single-cell RNA-seq denoising | SAVER-X – Laboratory for single Cell data science | R package for transfer learning of scRNA-seq denoising. Take a look at our free SAVER-X web-server for the transfer learning online computation! We also encourage you to read our pre-print manucript for more information. You can also refer to our earlier denoising method SAVER | Laboratory for single Cell data science | Where Statistics, Biology and Computer Science Meet | Uploading Data is as Easy as 1-2-3: | Researchers can directly upload their data of UMI counts to the web portal as a (gene x cell) matrix stored in a .csv, .txt or .rds file. Our cloud service does not store the user’s data or use it for any other purpose besides denoising | In most single cell transcriptomics (scRNA-seq) studies, the data are extremely sparse and noisy, hindering downstream analyses
feature list: operation 3501
feature list: operation 3557

SAXSDom
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0154
application sub category: topic_0196
application sub category: topic_0736
application sub category: topic 3474
citation: prot.25865
citation: pmcid:PMC7230021
citation: pubmed:31860156
description: Modeling multidomain protein structures using small-angle X-ray scattering data. This is a bioinformatics tool to use SAXS data to assemble protein domain structures into full-length structural models. Installation (tested on CentOS Linux 7 (Core)). (3) Compile SAXSDom from source code (required). running /data/jh7x3/SAXSDom/db_tools/tools/cmake-2.8.12.2/bin/cmake -E create_symlink "/data/jh7x3/SAXSDom/installation/Mocapy++-1.07/examples/data" "/data/jh7x3/SAXSDom/installation/Mocapy++-1.07/examples/data" 2>&1
feature list: operation_0303
feature list: operation_0310
feature list: operation_0321
feature list: operation_0476
feature list: operation_0477

SAnDReS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic 2275
application sub category: topic 3474
citation: 978-1-4939-9752-7 10
citation: 978-1-4939-9752-7 16
citation: 978-1-4939-9752-7 4
citation: pubmed:31452098
citation: pubmed:31452104
citation: pubmed:31452110
description: > CORRECT NAME OF TOOL COULD ALSO BE 'statistical analysis docking results', 'affinity', 'protein-targeted', 'machine-learning' | A Computational Tool for Docking | Molegro Virtual Docker for Docking | Machine Learning to Predict Binding Affinity | Make molecular docking reliable, fast, easy, free, and funny with SAnDReS. It is the easiest way to run dependable protein-ligand docking simulations. SAnDReS takes a different approach to docking; it focuses on the simulation of a system composed of an ensemble of crystallographic structures for which ligand binding affinity data is available
feature list: operation_0482
feature list: operation 3659
feature list: operation 3899
license: GPL-3.0

SBL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3517
citation: BTZ244
citation: pubmed:31081037
description: Coordinate Descent Approach for Sparse Bayesian Learning in High Dimensional QTL Mapping and Genome-wide Association Studies.
feature list: operation_0282
feature list: operation 3196
feature list: operation 3232
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Meiyue Wang

SBM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 3172
application sub category: topic 3512
citation: F1000RESEARCH.18705.2
citation: pmcid:PMC6743255
citation: pubmed:31559017
description: Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models | SBM-for-correlation-based-networks
feature list: operation 3439
feature list: operation 3463
feature list: operation 3766
license: GPL-3.0

SBML2Modelica
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0202
application sub category: topic_0602
application sub category: topic 3314
application sub category: topic 3379
application sub category: topic 3407
citation: BTZ860
citation: pubmed:31738386
description: SBML2Modelica is a tool which translates biochemical models written in System Biology Markup Language (SBML) Version 3 Level 2 into well-structured, user-intelligible, easily-modifiable Modelica models.
feature list: operation_0337
feature list: operation 3562

SBMLLint
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0821
application sub category: topic 2259
application sub category: topic 3292
application sub category: topic 3306
citation: https://doi.org/10.1101/816876
description: SBMLLint is a collection of tools for linting reactions. The initial focus is detecting mass balance errors. The tool takes as input a model expressed in either SBML (Systems Biology Markup Language, a standard format for biochemical models) or the Antimony language (a human readable representation of chemical reaction models).
feature list: operation 3096
feature list: operation 3660
license: MIT

SBP_2019
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/762773
description: > MEDIUM CONFIDENCE! | Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq | Code for producing the analysis in the "Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq" manuscript | Code for producing the analysis in the "Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq" by Valentine Svensson, Eduardo Beltrame and Lior Pachter | The workflow has 4 steps. The output data after each step can be downloaded from CaltechDATA at https://data.caltech.edu/records/1276 | 1) FASTQ Subsampling and processing with kallisto bus
feature list: operation 3223
feature list: operation 3230
feature list: operation 3800

SCALE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
application sub category: topic 3173
application sub category: topic 3474
citation: S41467-019-12630-7
citation: pmcid:PMC6783552
citation: pubmed:31594952
description: SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Single-cell ATAC-seq analysis via Latent feature Extraction. SCALE neural network is implemented in Pytorch framework. Lei Xiong, Kui Xu, Kang Tian, Yanqiu Shao, Lei Tang, Ge Gao, Michael Zhang, Tao Jiang & Qiangfeng Cliff Zhang. SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nature Communications, (2019).
feature list: operation 3432
feature list: operation 3435
feature list: operation 3557
feature list: operation 3891
license: MIT

SCANVIS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3512
citation: btz452
citation: pmcid:PMC6853764
citation: pubmed:31197308
description: Set of tools for SCoring, ANnotating and VISualizing splice junctions using annotation details (gencode or other).
feature list: operation 2939
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: SCANVIS-manual.pdf
software version: 0.99.15
primary contact: Phaedra Agius

SCATTER PHY
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3318
application sub category: topic 3474
citation: PREPRINTS201910.0115.V1
description: An Open Source Physical Layer for the DARPA Spectrum Collaboration Challenge.
feature list: operation 3215

SCDO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3063
application sub category: topic 3474
citation: BAZ118
citation: pmcid:PMC6878945
citation: pubmed:31769834
description: The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD and 3) link to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
feature list: operation 3096
feature list: operation 3435

SCDevDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3512
citation: FGENE.2019.00903
citation: pmcid:PMC6775478
citation: pubmed:31611909
description: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database
feature list: operation 2495
feature list: operation 3096
feature list: operation 3223

SCEptRe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2814
application sub category: topic 2830
application sub category: topic 3489
citation: S12859-019-3109-6
citation: pmcid:PMC6785892
citation: pubmed:31601176
description: SCEptRe provides weekly updated, non-redundant, user customized benchmark datasets with information on the immune receptor features for receptor-specific epitope predictions. This tool extracts weekly updated 3D complexes of antibody-antigen, TCR-pMHC and MHC-ligand from the Immune Epitope Database (IEDB) and clusters them based on antigens, receptors and epitopes to generate benchmark datasets. Users can customize structural quality and clustering parameters (e.g. resolution, R free factors, antigen or epitope sequence identity) to generate these datasets based on their need.
feature list: operation_0252
feature list: operation_0416
feature list: operation 3432

SCGid
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic_0621
application sub category: topic 3174
citation: BTZ866
citation: pubmed:31764940
description: consensus approach to contig filtering and genome prediction from single cell sequencing libraries of uncultured eukaryotes. SCGid, a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries. Please note that this version of SCGid constitutes an early-release version that is currently under active development toward a stable version coinciding with the release of the accepted manuscript introduing it. I am now porting SCGid to python 3 and stabilizing it for full release as SCGid (v1.0) within the next few weeks. This development is taking place on a separate branch. In the mean time, this beta version is working and available for use. I am available to assist with any problems you run into while using this branch of SCGid as well as patch bugs. If you encounter a bug or confusing error while running the beta version of SCGid, please open an issue on this repositiory
feature list: operation_0525
feature list: operation 3192
feature list: operation 3216
feature list: operation 3695
license: GPL-3.0

SCHEMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic 2830
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: https://doi.org/10.1101/834549
description: Schema is a general algorithm for integrating heterogeneous data modalities, with application to multi-modal single-cell biological datasets.
feature list: operation 3435
feature list: operation 3561
feature list: operation 3891

SCIFIL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0199
application sub category: topic 2640
citation: BTZ392
citation: pmcid:PMC6612866
citation: pubmed:31510696
description: Inference of clonal selection in cancer populations using single-cell sequencing data | Single Cell Inference of FItness Landscape | We propose a computational method for in vivo inference of clonal selection and estimate of fitness landscapes of heterogeneous cancer cell populations from single cell sequencing data | matlab -nodisplay -nodesktop -r "n=<number>;m=<number>;gv_file='<input_gv_tree>';output='<output_file>';method='<method_name>';nRep=<number>;theta=<number>;SCIFIL"
feature list: operation_0487
feature list: operation 3478
feature list: operation 3799
license: MIT

SCIMAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0610
application sub category: topic 3810
application sub category: topic 3855
citation: J.JENVMAN.2019.109366
citation: pubmed:31494409
description: Identifying critical source areas using multiple methods for effective diffuse pollution mitigation | A framework for modelling and mapping diffuse pollution risk across landscapes | SCIMAP - Diffuse Pollution Risk Mapping | To identify the locations that are a problem, we developed SCIMAP. This project was originally jointly developed between Durham and Lancaster Universities. SCIMAP is supported by the U.K.’s Natural Environment Research Council, the Eden Rivers Trust, the Department of the Environment, Food and Rural Affairs and the Environment Agency. Following this project SCIMAP has been supported by Durham University, the Rivers Trust and the Environment Agency
feature list: operation 2429
feature list: operation 3501

SCMVTDb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3308
citation: J.YGENO.2019.11.017
citation: pubmed:31770586
description: Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach.
feature list: operation_0524
feature list: operation 1781
feature list: operation 3258

SCMarker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: JOURNAL.PCBI.1007445
citation: pmcid:PMC6837541
citation: pubmed:31658262
description: Ab initio marker selection for single cell transcriptome profiling. Marker gene selection from scRNA-seq data. SCMarker performs cell-type-specific marker selection from single cell RNA sequencing data. It provides users a tool for selecting features from tens of thousands of genes for further cell-type clustering analysis
feature list: operation_0313
feature list: operation 3501

SCNBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0621
application sub category: topic_0780
application sub category: topic 2885
application sub category: topic 3170
citation: BAZ111
citation: pmcid:PMC6853641
citation: pubmed:31680133
description: a genomics portal for the soybean cyst nematode (Heterodera glycines). All supporting analyses required for SCNBase data
feature list: operation_0362
feature list: operation_0433
feature list: operation 2421

SCOC database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0219
application sub category: topic 3068
application sub category: topic 3387
application sub category: topic 3489
citation: S41597-019-0259-3
citation: pmcid:PMC6820755
citation: pubmed:31664032
description: SCOC database is a large, open, and global database with sediment community oxygen consumption rates.
feature list: operation 2421
feature list: operation 3431

SCOM
type: SoftwareApplication
input: Expression data
  type: FormalParameter
  additional type: data 2603
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
application sub category: topic 3307
description: SCOM applies three criteria (significantly synergistic competition for mRNAs, significantly positive correlation, and significantly sensitive correlation conditioning on synergistically competed mRNAs) to predict ncRNA synergistic competition network from gene (ncRNAs acting as ceRNAs, and target mRNAs) expression data and predicted ncRNA-related ceRNA networks.
feature list: operation_0313
feature list: operation 2437
feature list: operation 2495
feature list: operation 3463
feature list: operation 3927
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0

SCOPA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic_0820
application sub category: topic 3517
citation: s12859-016-1437-3
citation: pmcid:PMC5225593
citation: pubmed:28077070
description: Software for COrrelated Phenotype Analysis.
feature list: operation 3196
feature list: operation 3557
feature list: operation 3659
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
software help: tutorial
software version: 1.0.14
primary contact: Andrew P Morris
primary contact: Reedik Magi

SCOPIT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0622
application sub category: topic 3308
citation: s12859-019-3167-9
citation: pmcid:PMC6852764
citation: pubmed:31718533
description: Tool for sample size calculations for single-cell sequencing experiments.
feature list: operation 2238
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: scs power multinomial

SCRABBLE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 3170
application sub category: topic 3308
citation: s13059-019-1681-8
citation: pmcid:PMC6501316
citation: pubmed:31060596
description: Single-cell RNA-seq imputation constrained by bulk RNA-seq data.
feature list: operation 3436
feature list: operation 3557
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: SCRABBLE.pdf
software help: my-vignette.pdf
primary contact: Tao Peng

SCRIBE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3518
citation: https://doi.org/10.1101/793463
description: a new approach to dropout imputation and batch effects correction for single-cell RNA-seq data. Please run Rscript --vanilla fitSCRIBE.R [expression file] [batch index file] [biological group index file] [output file]
feature list: operation 2495
feature list: operation 3557

SCRIBER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic 2275
citation: BTZ324
citation: pmcid:PMC6612887
citation: pubmed:31510679
description: accurate and partner type-specific prediction of protein-binding residues from proteins sequences | SCRIBER - web server from Biomine lab
feature list: operation_0272
feature list: operation 2492
feature list: operation 3899

SCSsim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0632
application sub category: topic 2885
application sub category: topic 3168
citation: btz713
citation: pmcid:PMC7703785
citation: pubmed:31584615
description: SCSsim is a tool designed for emulating single-cell genome sequencing data. It consists of three modules: 1) “simuVars” module aims to generate single cell genome from a given reference sequence by inserting user-defined genomic variations into genomic loci; 2) “learnProfile” component is developed to infer sequencing platform dependent profiles from real data; 3) “genReads” utility is provided to mimic single-cell genome amplification and read generation procedures based on the results of “simuVars” and “learnProfile”.
feature list: operation_0296
feature list: operation 3198
license: BSD-3-Clause

SCTree
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
citation: BTZ425
citation: pubmed:31116393
description: Statistical test of structured continuous trees based on discordance matrix.
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Liang Ma
primary contact: Lin Wan

SCeNGEA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3067
application sub category: topic 3304
application sub category: topic 3308
citation: https://doi.org/10.1101/737577
description: Expression profiling of the mature C. elegans nervous system by single-cell RNA-Sequencing | Abstract A single neuron and its synapses define the fundamental structural motif of the brain but the underlying gene expression programs that specify individual neuron types are poorly understood. To address this question in a model organism, we have produced a gene expression profile of >90% of the individual neuron classes in the C. elegans nervous system, an ensemble of neurons for which both the anatomy and connectivity are uniquely defined at single cell resolution. We generated single cell transcriptomes for 52,412 neurons that resolve as clusters corresponding to 109 of the canonical 118 neuron classes in the mature hermaphrodite nervous system. Detailed analysis revealed molecular signatures that further subdivide identified classes into specific neuronal subtypes
feature list: operation 2495
feature list: operation 3891

SCryPTA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0153
application sub category: topic 2828
application sub category: topic 3318
citation: https://doi.org/10.1101/791848
description: A web-based platform for analyzing Small-Angle Scattering curves of lyotropic liquid crystals. Small Angle Scattering Crystallographic Peak Treatment and Analysis. To access SCryPTA, click here . The instructions to use SCryPTA can be found here
feature list: operation 3454

SDE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 2269
application sub category: topic 3068
application sub category: topic 3399
citation: https://doi.org/10.1101/635177
description: Adding noise to Markov cohort state-transition models.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: readme.md
primary contact: Rowan Iskandar

SDEAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3512
citation: btw513
citation: pubmed:27522083
description: Splice graph based differential transcript expression analysis tool for population data.
feature list: operation 2495
feature list: operation 3223
is accessible for free: true
license: Unlicense
operating system: Linux
software help: wiki
primary contact: Ei-Wen Yang
primary contact: Tao Jian

SDG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 3489
citation: F1000RESEARCH.20233.1
description: A Sequence Distance Graph framework for genome assembly and analysis | Sequence Distance Graph framework: graph + reads + mapping + analysis | The Sequence Distance Graph (SDG) is a framework to work with genome graphs and sequencing data. It provides a workspace built around a Sequence Distance Graph, datastores for paired, linked and long reads, read mappers, and k-mer counters. It can be used to perform different types of sequence analyses | Index of /opendata/data/sdg_datasets | Welcome to SDG’s documentation! — SDG documentation | Websites for you and your projects, hosted directly from your GitHub repository. Just edit, push, and your changes are live | Websites for you and your projects | Hosted directly from your GitHub repository. Just edit, push, and your changes are live | Ready to get started? Build your own site from scratch or generate one for your project
feature list: operation_0524
feature list: operation_0525
feature list: operation 3216
license: MIT
software help: sdg examples

SDM6A
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3295
application sub category: topic 3315
application sub category: topic 3474
citation: J.OMTN.2019.08.011
citation: pmcid:PMC6796762
citation: pubmed:31542696
description: A Web-Based Integrative Machine-Learning Framework for Predicting 6mA Sites in the Rice Genome | Welcome to the Home Page of SDM6A | For the convenience of users, particularly for the vast majority of experimental scientists, a publicly accessible web-server for SDM6A has been established. Moreover, to maximize users' convenience, given below a step-by-step guide on how to use it to get the desired results without the need to through the above mathematical details
feature list: operation 3501
software help: SDM6Atutorial.html

SDR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3068
citation: PEERJ.PREPRINTS.2227V2
description: A GRASS tool for the Sediment Delivery Ratio mapping. This work involves a tool implementation for evaluating Sediment Delivery Ratio (SDR) in a river basin, through GRASS GIS software. The definition of a spatially distributed value of SDR is a very important task as the sediment routing can affects solid transport in stream channels, water quality degradation, and frequency increase of natural disasters such as debris flows and mudflows. For such reason the SDR evaluation, coupled with GIS approach, has been extensively used in scientific literature. Geographic information systems provide a fundamental support for a better prediction of SDR, since it can consider the space variability of factors influencing the sediment routing processes. Actually a specific GIS module to estimate the spatial variability of SDR does not exist.
feature list: operation 2429

SDRS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3305
application sub category: topic 3322
application sub category: topic 3519
citation: JOURNAL.PONE.0223544
citation: pmcid:PMC6795434
citation: pubmed:31618236
description: The Swine Disease Reporting System (SDRS) consists of multiple projects that aggregates data from participating veterinary diagnostic laboratories (VDLs) in the United States of America, and reports the major findings to the swine industry.
feature list: operation 3196
feature list: operation 3283
feature list: operation 3436

SE-DMTG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0749
citation: S12864-019-5956-Y
citation: pmcid:PMC6686515
citation: pubmed:31390979
description: > MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations | BACKGROUND:The detection of protein complexes is of great significance for researching mechanisms underlying complex diseases and developing new drugs. Thus, various computational algorithms have been proposed for protein complex detection. However, most of these methods are based on only topological information and are sensitive to the reliability of interactions. As a result, their performance is affected by false-positive interactions in PPINs. Moreover, these methods consider only density and modularity and ignore protein complexes with various densities and modularities
feature list: operation 2492
feature list: operation 3501

SEAMIS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3489
application sub category: topic 3678
citation: J.DIB.2019.104600
citation: pmcid:PMC6817659
citation: pubmed:31673594
description: Relative sea-level data from the SEAMIS database compared to ICE-5G model predictions of glacial isostatic adjustment.
feature list: operation_0337
feature list: operation 3435
license: GPL-3.0

SEAweb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3360
application sub category: topic 3512
citation: gkz869
citation: pmcid:PMC6943056
citation: pubmed:31598718
description: the small RNA Expression Atlas web application. Sign in with Google or with you SEA account below. If you have not created an account yet, then please register first. If you have received an eMail from Oasis 2 that the classification or DE analysis results are downloadable, you can provide the given link here, in order to upload the output to this system and compare them with publically available datasets. SEA (also SEAweb) is a searchable database for the expression of small RNA (miRNA, piRNA, snoRNA, snRNA, siRNA) and pathogens. Publically available sRNA sequencing datasets were analysed with Oasis 2 pipelines and the results are stored here for easy and comparable search. Our curated, ontology connected metadata enables powerful searches within this database. Learn more in the documentation and publication
feature list: operation_0463
feature list: operation 2421
feature list: operation 3792

SECAPR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0769
application sub category: topic 3168
application sub category: topic 3293
application sub category: topic 3512
citation: PEERJ.PREPRINTS.26477V2
citation: PEERJ.PREPRINTS.26477V3
description: A bioinformatics pipeline for the rapid and user-friendly processing of Illumina sequences, from raw reads to alignments. A bioinformatics pipeline for the rapid and user-friendly alignment of hybrid enrichment sequences, from raw reads to alignments. Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics. SEquence CApture PRocessor (SECAPR). Sorry, something went wrong. Reload?. Sorry, we cannot display this file. We are now teaching a free 1-week intensive course on target enrichment data, including practical exercises for all functionalities of the SECAPR pipeline. See course overview from last year and contact tobias.andermann@bioenv.gu.se in case you are interested. Sorry, this file is invalid so it cannot be displayed
feature list: operation_0310
feature list: operation 3192
feature list: operation 3198
feature list: operation 3454
license: MIT
software help: documentation.ipynb

SECLAF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
additional type: Web service
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic_0623
citation: bty116
citation: pubmed:29490010
description: Webserver and deep neural network design tool for hierarchical biological sequence classification.
feature list: operation 2995
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Balázs Szalkai
primary contact: Vince Grolmusz

SECNVs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3315
application sub category: topic 3673
application sub category: topic 3676
citation: https://doi.org/10.1101/824128
description: A Simulator of Copy Number Variants and Whole-Exome Sequences from Reference Genomes. A tool for simulating CNVs for WES data. It simulates rearranged genome(s), short reads (fastq) and BAM file(s) automatically in one single command. SECNVs 2.7.1 (SimulateCNVs 2.7.1). SECNVs (Simulator of Exome Copy Number Variants) is a fast, robust and customizable software application for simulating copy number variants and whole-exome sequences from a reference genome
feature list: operation 3196
feature list: operation 3211
feature list: operation 3227
feature list: operation 3228
license: MIT

SED
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic 3474
citation: BTZ336
citation: pmcid:PMC6612825
citation: pubmed:31510691
description: Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors | SED: Screening for Lasso of ECFPs and Deep Neural Nets | SED was developed to predict ligand bioactivities and to recognize key substructures associated with GPCRs through the coupling of screening for Lasso of long extended-connectivity fingerprints (ECFPs) with deep neural network training
feature list: operation_0482

SEGAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3382
application sub category: topic 3474
application sub category: topic 3810
citation: PREPRINTS201912.0028.V1
description: SEGAN is a novel diversity-generated image inpainting adversarial network with a newly designed style extractor for diversity image inpainting tasks. For a single input image with missing regions, our model can generate numerous diverse results with plausible content. Experiments on various datasets have shown that our results are diverse and natural, especially for images with large missing areas.
feature list: operation 3443

SELVa
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0199
citation: https://doi.org/10.1101/647834
description: SELVa (Simulator of Evolution with Landscape Variation) - simulator of sequence evolution that allows the fitness landscape to vary according to user-specified rules.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: SELVa manual.pdf

SEMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0611
application sub category: topic 2640
application sub category: topic 3473
citation: btz303
citation: pmcid:PMC6821276
citation: pubmed:31070723
description: > COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/gddp (RESEARCH.CCHMC.ORG) | > CORRECT NAME OF TOOL COULD ALSO BE 'CONCLUSION:SEMA' | Graphical data mining of cancer mechanisms with SEMA | SEMA is a graphical hypothesis testing platform for multidimensional cancer genomics data | SEMA is a graphical hypothesis testing platform for multidimensinoal cancer genomics data, written in R Shiny and JavaScript. SEMA uses Structural Equation Modeling (SEM) for the analyses of graphical models | Free HTML5 Template by FreeHTML5.CO | Graphical data mining from cancer genomic datasets
feature list: operation_0306
feature list: operation 2238
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: SEMA Tutorial.pdf
primary contact: Kakajan Komurov

SEMpl
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 2885
application sub category: topic 3169
citation: btz612
citation: pmcid:PMC7999143
citation: pubmed:31373606
description: Predicting the effects of SNPs on transcription factor binding affinity | MOTIVATION:GWAS have revealed that 88% of disease associated SNPs reside in noncoding regions. However, noncoding SNPs remain understudied, partly because they are challenging to prioritize for experimental validation. To address this deficiency, we developed the SNP effect matrix pipeline (SEMpl). RESULTS:SEMpl estimates transcription factor binding affinity by observing differences in ChIP-seq signal intensity for SNPs within functional transcription factor binding sites genome-wide. By cataloging the effects of every possible mutation within the transcription factor binding site motif, SEMpl can predict the consequences of SNPs to transcription factor binding. This knowledge can be used to identify potential disease-causing regulatory loci
feature list: operation_0420
feature list: operation_0445
feature list: operation 3661

SEPAS
type: SoftwareApplication
input: Protein atom
  type: FormalParameter
  additional type: data 1755
  encoding format: format 1475
output: Text data
  type: FormalParameter
  additional type: data 2526
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic 2814
application sub category: topic 3306
citation: acs.jproteome.9b00594
citation: https://doi.org/10.1080/07391102.2019.1662328
citation: pubmed:31476974
citation: pubmed:31795635
description: Now to predict the experimentally measured affinity between protein monomers in solution, we just need the 3D structure of the suggested PBP on one subunit of the proposed dimer.
feature list: operation 2423
is accessible for free: true
operating system: Linux
software help: affinity
software version: SEPAS_V1, Dec 2019

SEPATH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0637
application sub category: topic_0769
application sub category: topic 2640
application sub category: topic 3174
application sub category: topic 3316
citation: S13059-019-1819-8
citation: pmcid:PMC6805339
citation: pubmed:31639030
description: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines. SEPATH template pipelines optimised for UEA high performance computing cluster. SEPATH - Searching for Pathogens Computational Pipeline. A repository containing scripts and results required for the SEPATH manuscript. SEPATH is a software designed to obtain accurate taxonomic classifications from within host tissue sequences. It is implemented in python 3 and relies on the Snakemake workflow management system. SEPATH was produced specifically to provide researchers with the ability to conduct ultra high throughput metagenomic studies from raw data to classification and has been benchmarked on simulated human cancer whole genome sequence datasets
feature list: operation_0310
feature list: operation_0335
feature list: operation_0337
feature list: operation 3192
feature list: operation 3460
license: GPL-3.0

SEQdata-BEACON
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 2269
application sub category: topic 3168
application sub category: topic 3489
citation: S13040-019-0209-9
citation: pmcid:PMC6857306
citation: pubmed:31807141
description: SEQdata-BEACON is a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500.
feature list: operation_0337
feature list: operation 2426
feature list: operation 3659

SEQing
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3794
citation: https://doi.org/10.1101/2019.12.17.865873
description: web-based visualization of Arabidopsis thaliana iCLIP and RNA-seq data in an interactive python framework. SEQing: interactive web-based tool for visualization of iCLIP and RNA-seq data. The file requirements.txt can be used to install all needed needed dependencies for the project. Python 3.5 or higher is required and we recommend to setup a virtual environment for this project. If your current python points to a python2 version, please put python3 instead of just python before running SEQing
feature list: operation_0337
feature list: operation 2499
license: MIT

SEQprocess
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0769
application sub category: topic 3170
application sub category: topic 3676
citation: s12859-019-2676-x
citation: pmcid:PMC6383233
citation: pubmed:30786880
description: Modularized and customizable pipeline framework for NGS processing in R package.
feature list: operation 3192
feature list: operation 3211
feature list: operation 3219
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: Reference Manual.pdf
software help: vignettes.pdf

SEQualyzer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0097
application sub category: topic_0099
application sub category: topic 3308
citation: btw627
citation: pmcid:PMC6075182
citation: pubmed:28172632
description: SEQualyzer (Structure-profiling Experiment Quality Analyzer ) - interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data.
feature list: operation 2428
feature list: operation 2495
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: SEQualyzer Manual.pdf
primary contact: Sharon Aviran

SEVA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic_0654
application sub category: topic_0798
application sub category: topic 3301
application sub category: topic 3895
citation: GKZ1024
citation: pubmed:31740968
description: The Standard European Vector Architecture (SEVA) platform is a web-based resource and a material clone repository to assist the choice of optimal plasmid vectors for de-constructing and re-constructing complex prokaryotic phenotypes.
feature list: operation_0310
feature list: operation_0578
feature list: operation 3431
feature list: operation 3435
software version: 3.0

SF-Matching
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3047
application sub category: topic 3172
application sub category: topic 3474
application sub category: topic 3520
citation: BTZ736
citation: pubmed:31605112
description: SF-Matching(SubFragment-Matching) is a machine-learning based approach to predict compounds from tandem mass spectra.
feature list: operation 3431
feature list: operation 3797
feature list: operation 3803
feature list: operation 3860

SFLA IWSSr
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3474
application sub category: topic 3518
citation: S41598-019-54987-1
citation: pmcid:PMC6901457
citation: pubmed:31819106
description: SFLA IWSSr is an Efficient hybrid filter-wrapper metaheuristic-based gene selection method for high dimensional datasets.
feature list: operation 3454
feature list: operation 3695
feature list: operation 3891

SGID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0605
application sub category: topic 3173
application sub category: topic 3308
citation: https://doi.org/10.1101/739961
description: a comprehensive and interactive database of the silkworm | Silkworm Genome Informatics Database | e.g. FIBH or KWMTBOMO15365 or BGIBMGA005111 or silk fibroin heavy chain &nbspBrowse in Gene Lists | Search by sequence alignment against genomes or genes | With the Exponential increasing of sequencing data in genomics, transcriptomics and epigenetics, and the development of data analysis methods, a serious of informatics database with integrated analysis tools have been constructed, like the Flybase and TAIR. Silkworm, as a domesticated insect, lacks an online analysis platform. On the basis of previous efforts, including Silkbase, SilkDB and Ensembl Insects, we constructed the silkworm genome informatics database, SGID. Hopefully, it will assist to bioinformatics analysis of silkworms in the future
feature list: operation_0313
feature list: operation_0533
feature list: operation 3501

SGL-SVM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3168
application sub category: topic 3303
application sub category: topic 3518
citation: J.JTBI.2019.110098
citation: pubmed:31786183
description: A novel method for tumor classification via support vector machine with sparse group Lasso. At present, with the in-depth study of gene expression data, the significant role of tumor classification in clinical medicine has become more apparent. In particular, the sparse characteristics of gene expression data within and between groups. Therefore, this paper focuses on the study of tumor classification based on the sparsity characteristics of genes. On this basis, we propose a new method of tumor classification-Sparse Group Lasso (least absolute shrinkage and selection operator) and Support Vector Machine (SGL-SVM). Firstly, the primary selection of feature genes is performed on the normalized tumor datasets using the Kruskal-Wallis rank sum test. Secondly, using a sparse group Lasso for further selection, and finally, the support vector machine serves as a classifier for classification. We validate proposed method on microarray and NGS datasets respectively
feature list: operation 3435

SHYBRID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0632
application sub category: topic_0749
application sub category: topic 3304
citation: https://doi.org/10.1101/734061
description: > MEDIUM CONFIDENCE! | A graphical tool for generating hybrid ground-truth spiking data for evaluating spike sorting performance | SHYBRID is a graphical user interface that allows for the easy creation of hybrid ground truth extracellular recordings. This README file contains information on how to install the program, as well as information on how to get started making extracellular spiking ground truth data. If you have any further questions feel free to contact me
feature list: operation_0337
feature list: operation 2422
feature list: operation 3802
license: GPL-3.0

SIAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3375
citation: bty1069
citation: pubmed:30601937
description: Software for Structural Identifiability ANalysis of ODE models.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Gleb Pogudin

SIIM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3063
application sub category: topic 3303
application sub category: topic 3384
application sub category: topic 3474
citation: s10278-019-00292-2
citation: pmcid:PMC7165230
citation: pubmed:31713070
description: SIIM is a professional organization at the nexus of medical imaging informatics and healthcare technologies. SIIM provides an unparalleled opportunity to not only hear from the best, brightest and most forward thinkers in imaging space but talk to them face to face in a collegial setting.
feature list: operation 3435
feature list: operation 3443

SIMLIN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic_0749
application sub category: topic 3474
citation: S12859-019-3178-6
citation: pmcid:PMC6868744
citation: pubmed:31752668
description: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models. SIMLIN: an improved bioinformatics approach based on multi-stage ensemble learning model for S-sulphenylation prediction
feature list: operation_0253
feature list: operation_0267
feature list: operation_0417

SINBAD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic 2640
application sub category: topic 3320
citation: https://doi.org/10.1101/623876
description: Survival-significant Isoform Networks By Altered Domain-inclusion.
feature list: operation 2499
feature list: operation 3359
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Sean West

SINE_scan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0780
application sub category: topic 3500
citation: btw718
citation: pmcid:PMC5408816
citation: pubmed:28062442
description: Tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets.
feature list: operation 3798
is accessible for free: true
license: Unlicense
operating system: Linux
software help: README.md
primary contact: Hao Wang

SINGLe
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 2546
  encoding format: format 2572
output: Sequence signature data
  type: FormalParameter
  additional type: data_0860
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3168
application sub category: topic 3895
application sub category: topic 3912
description: Accurate consensus sequence from nanopore reads of a DNA gene library. SINGLe corrects for systematic errors in nanopore sequencing reads of gene libraries and it retrieves true consensus sequences of variants identified by a barcode, needing only a few reads per variant.
feature list: operation 2403
feature list: operation 3219
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: single.pdf

SIRM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0593
application sub category: topic_0602
application sub category: topic 3172
application sub category: topic 3407
application sub category: topic 3520
citation: https://doi.org/10.1101/839241
description: Robust Moiety Model Selection Using Mass Spectrometry Measured Isotopologues.
feature list: operation 3629
feature list: operation 3660
feature list: operation 3803

SISTR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 2830
application sub category: topic 3305
application sub category: topic 3500
application sub category: topic 3673
citation: aem.02265-19
citation: pmcid:PMC7028957
citation: pubmed:31862714
description: The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching.
feature list: operation_0337
feature list: operation_0525
feature list: operation 3840
is accessible for free: true
license: Apache-2.0
software version: 1.1.2

SJARACNe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3518
citation: bty907
citation: pmcid:PMC6581437
citation: pubmed:30388204
description: Scalable software tool for gene network reverse engineering from big data.
feature list: operation 2495
feature list: operation 2497
feature list: operation 3439
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Yu Lab in the Department of Computational Biology at St. Jude Children's Research Hospital

SKCMhrp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 2830
application sub category: topic 3170
application sub category: topic 3676
citation: https://doi.org/10.1101/850677
description: Computing Skin Cutaneous Melanoma Outcome from the HLA-alleles and Clinical Characteristics. Skin Cutaneous Melanoma High-Risk Prediction(SKCMhrp) webserver can be used to distinguish high risk SKCM patients from low risk SKCM patients from their HLA-superallele and clinical characteristics. The risk estimation is based on statistical and survival analysis on recent SKCM datasets. See general section for more information.
feature list: operation_0252
feature list: operation 3503
feature list: operation 3659
software help: data.php

SKIMMR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic_0634
application sub category: topic 3070
application sub category: topic 3384
citation: PEERJ.PREPRINTS.352V3
citation: pmcid:PMC4121546
citation: pubmed:25097821
description: Facilitating knowledge discovery in life sciences by machine-aided skim reading. SKIMMR - a research prototype for machine-aided skim reading (includes back-end code for generating a graph-like knowledge base from texts and a standalone HTTP server-based UI)
feature list: operation_0306
feature list: operation 1812
feature list: operation 2421
license: GPL-3.0

SLAM-DUNK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 2885
application sub category: topic 3168
citation: S12859-019-2849-7
citation: pmcid:PMC6528199
citation: pubmed:31109287
description: Fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.
feature list: operation_0484
feature list: operation 2495
feature list: operation 3799
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: slam-dunk
primary contact: https://orcid.org/0000-0003-3908-4224
primary contact: Philipp Rescheneder

SLAST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic 3168
citation: https://doi.org/10.1101/840546
description: Simple Local Alignment Search Tool.
feature list: operation_0491
feature list: operation_0495
feature list: operation 2421

SLE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0203
application sub category: topic_0634
application sub category: topic 3360
application sub category: topic 3518
citation: BTZ758
citation: pubmed:31598632
description: Single-sample landscape entropy reveals the imminent phase transition during disease progression.
feature list: operation 3435
feature list: operation 3439
feature list: operation 3454

SLIDE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic_0602
application sub category: topic 3068
application sub category: topic 3512
citation: bty534
citation: pmcid:PMC6330001
citation: pubmed:29955804
description: Systems-Level Interactive Data Exploration (SLIDE) - web-based tool for interactive visualization of large-scale – omics data.
feature list: operation 3501
is accessible for free: true
license: BSD-2-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Hyungwon Choi

SLIM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0610
application sub category: topic_0769
application sub category: topic 3168
citation: s12859-019-2663-2
citation: pmcid:PMC6381720
citation: pubmed:30782112
description: Web application for the reproducible processing of environmental DNA metabarcoding data.
feature list: operation_0450
feature list: operation 3185
feature list: operation 3200
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: SLIM
primary contact: Yoann Dufresne

SLR-superscaffolder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic 3168
citation: https://doi.org/10.1101/762385
description: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme | A scaffold assemble pipeline for stLFR reads | This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds | git clone --recursive https://github.com/BGI-QingDao/SLR-superscaffolder.git YOUR-DOWNLOAD-DIR --depth 10 | Here is an illustration of this pipeline:
feature list: operation_0524
feature list: operation 3216
feature list: operation 3798

SLTChemDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 2258
application sub category: topic 2840
application sub category: topic 3343
citation: S41598-019-43559-Y
citation: pmcid:PMC6509116
citation: pubmed:31073139
description: Database of Chemical Constitutents of Smokeless Tobacco Products.
feature list: operation 2421
feature list: operation 3431
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
primary contact: Harpreet Singh

SLiM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic_0610
application sub category: topic 3299
citation: https://doi.org/10.1086/723601
citation: msy228
citation: msy237
citation: https://doi.org/10.1101/2025.08.07.669155
citation: https://doi.org/10.1111/1755-0998.12968
citation: pmcid:PMC10793872
citation: pmcid:PMC12363870
citation: pmcid:PMC6389312
citation: pmcid:PMC6393187
citation: pmcid:PMC6501880
citation: pubmed:30517680
citation: pubmed:30565882
citation: pubmed:30590560
citation: pubmed:37130229
citation: pubmed:40832315
description: Evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Includes a graphical modeling environment.
feature list: operation_0230
feature list: operation_0550
feature list: operation 3946
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Eidos Manual.pdf
software help: SLiMEidosRefSheets.zip
software help: SLiM Manual.pdf
software version: 5.1
primary contact: https://orcid.org/0000-0001-8453-9377
primary contact: https://orcid.org/0000-0003-1874-8327

SM2RAIN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: PEERJ.PREPRINTS.2131V4
description: Using Python® language for the validation of the CCI soil moisture products via SM2RAIN.
feature list: operation 2428

SMAGEXP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3518
citation: giy167
citation: pmcid:PMC6354025
citation: pubmed:30698691
description: SMAGEXP (Statistical Meta-Analysis for Gene EXPression) - galaxy tool suite for transcriptomics data meta-analysis.
feature list: operation 3223
feature list: operation 3435
feature list: operation 3680
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Samuel Blanck

SMART App
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0654
application sub category: topic 2640
application sub category: topic 3295
citation: S13072-019-0316-3
citation: pmcid:PMC6894252
citation: pubmed:31805986
description: an interactive web application for comprehensive DNA methylation analysis and visualization. BACKGROUND:Data mining of The Cancer Genome Atlas (TCGA) data has significantly facilitated cancer genome research and provided unprecedented opportunities for cancer researchers. However, existing web applications for DNA methylation analysis does not adequately address the need of experimental biologists, and many additional functions are often required. RESULTS:To facilitate DNA methylation analysis, we present the SMART (Shiny Methylation Analysis Resource Tool) App, a user-friendly and easy-to-use web application for comprehensively analyzing the DNA methylation data of TCGA project
feature list: operation_0337
feature list: operation 2495
feature list: operation 3204

SMARTdenovo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
description: Ultra-fast de novo assembler using long noisy reads
feature list: operation_0524

SMARTp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3315
application sub category: topic 3399
application sub category: topic 3421
citation: bimj.201900027
citation: pmcid:PMC7054179
citation: pubmed:31531896
description: A SMART design for nonsurgical treatments of chronic periodontitis with spatially referenced and nonrandomly missing skewed outcomes | R codes for sample size calculation to detect dynamic treatment regime (DTR) effects based on changes in CAL outcomes from a non-surgical chronic periodontitis treatments study. The experiment is performed under a SMART design. The clustered tooth (sub-unit) level CAL outcomes are skewed, spatially-referenced, and non-randomly missing. The imple… | A SMART design for non-surgical treatments of chronic periodontitis with spatially-referenced and non-randomly missing skewed outcomes | devtools::install_github("bandyopd/SMARTp") | # Install from CRAN (when available)
feature list: operation 3557

SMIRNOFF99Frosst
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 3047
application sub category: topic 3292
application sub category: topic 3336
citation: acs.jctc.9b00748
citation: CHEMRXIV.9159872.V2
citation: pmcid:PMC7328435
citation: pubmed:31603667
description: Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.
feature list: operation 2476
feature list: operation 3893

SMOG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic 3070
citation: SHTI190814
citation: pubmed:31483262
description: > HOMEPAGE MISSING! | > NAME EQUAL TO (PUB. DIFFERENT) bio.tools/smog | A Lightweight Tool for Object-Spreadsheet Mapping | In the life science domain, experts are usually familiar with spreadsheet software and often use it in their daily work to collect and structure required domain knowledge. The processing and analysis of spreadsheet data is an important task that must be supported by efficient software solutions. A typical application scenario is for example an integration of spreadsheet data (specified or derived) in an ontology to provide reasoning or search. Different converter tools were developed to support a spreadsheet-to-ontology transformation. Such tools allow often only a relatively simple structure of the spreadsheet template or they require complex mapping processes to map the spreadsheet and ontological entities

SMSNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2830
application sub category: topic 3520
citation: MCP.TIR119.001656
citation: pmcid:PMC6885704
citation: pubmed:31591261
description: Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework. Sequence-Mask-Search framework and SMSNet model for de novo peptide sequencing. SMSNet's predictions for HLA peptidome and human phosphoproteome datasets. SMSNet's training datasets (WCU-MS-BEST, DeepNovo, ProteomeTools). SMSNet's training datasets (WCU-MS-ALL). Two models for SMSNet are provided here. SMSNet's predicted amino acid sequences for a public HLA peptidome dataset (MassIVE accession MSV000080527) and phosphoproteome dataset (PRIDE accession PXD009227) can be found on FigShare. SMSNet's predicted amino acid sequences for a public HLA peptidome dataset (MassIVE accession MSV000080527) and human phosphoproteome dataset (PRIDE accession PXD009227)
feature list: operation 3359
feature list: operation 3643
feature list: operation 3644
feature list: operation 3646
license: Apache-2.0
software help: https://figshare.com/articles/SMSNet_s_training_datasets_WCU-MS-ALL_/9738839
software help: https://figshare.com/articles/SMSNet_s_training_datasets_WCU-MS-BEST_DeepNovo_ProteomeTools_/9734105

SMT-Genetic
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0202
application sub category: topic 3304
application sub category: topic 3334
citation: https://doi.org/10.1101/626598
description: Identifying Brain Region Connectivity using Steiner Minimal Tree Approximation and a Genetic Algorithm Web-based tool to find a connectivity path among a given set of brain regions. Specifically, this tool uses a genetic algorithm to find a better connectivity path among the brain regions than SMT-Neurophysiology.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Dewan Sarwar

SMUT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3517
citation: btz285
citation: pmcid:PMC6853702
citation: pubmed:31099385
description: Multi-SNP mediation intersection-union test.
feature list: operation 3196
feature list: operation 3557
feature list: operation 3661
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: SMUT.pdf
primary contact: Wujuan Zhong

SMoLR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3382
citation: s12859-018-2578-3
citation: pmcid:PMC6334411
citation: pubmed:30646838
description: R package for visualization and analysis of single-molecule localization microscopy data.
feature list: operation 3457
feature list: operation 3799
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Maarten Paul

SNAPPy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3293
application sub category: topic 3305
citation: vez050
description: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing | SNAPPy is a Snakemake pipeline for HIV-1 subtyping by phylogenetic pairing | This is the repository for SNAPPy, a Snakemake pipeline for HIV-1 subtyping by phylogenetic pairing. SNAPPy allows high-throughput HIV-1 subtyping locally while being resource efficient and scalable. This pipeline was constructed using Snakemake , and it uses MAFFT and for multiple sequence alignment, BLAST for similarirty querys, IQ-TREE for phylogenetic inference, and several Biopython modules for data parsing an analysis. For in-depth information on how the tool works please visit the documentation page. SNAPPy was design for Linux based operative systems | Welcome to snappy’s documentation! — SNAPPy-HIV1-Subtyping 1.0.0 documentation | Free document hosting provided by Read the Docs
feature list: operation 1812
feature list: operation 3192
feature list: operation 3196
license: MIT
software help: snappy-hiv1-subtyping.readthedocs.io

SNOMED CT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0089
application sub category: topic 3325
application sub category: topic 3337
citation: pubmed:17911793
description: Web-based browser with comprehensive, scientifically validated clinical healthcare terminology. Enables consistent representation of clinical content in electronic health records.
feature list: operation 2422
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: five-step-briefing

SNP2APA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 2885
application sub category: topic 3517
citation: gkz793
citation: pmcid:PMC6943033
citation: pubmed:31511885
description: > HOMEPAGE BROKEN! | a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers | Alternative polyadenylation (APA) is an important post-transcriptional regulation that recognizes different polyadenylation signals (PASs), resulting in transcripts with different 3' untranslated regions, thereby influencing a series of biological processes and functions. Recent studies have revealed that some single nucleotide polymorphisms (SNPs) could contribute to tumorigenesis and development through dysregulating APA. However, the associations between SNPs and APA in human cancers remain largely unknown. Here, using genotype and APA data of 9082 samples from The Cancer Genome Atlas (TCGA) and The Cancer 3'UTR Altas (TC3A), we systematically identified SNPs affecting APA events across 32 cancer types and defined them as APA quantitative trait loci (apaQTLs). As a result, a total of 467 942 cis-apaQTLs and 30 721 trans-apaQTLs were identified
feature list: operation_0428
feature list: operation 3196

SNP2SIM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic 2275
citation: s12859-019-2774-9
citation: pmcid:PMC6448223
citation: pubmed:30943891
description: Modular workflow for standardizing molecular simulation and functional analysis of protein variants.
feature list: operation_0478
feature list: operation 2476
feature list: operation 3216
is accessible for free: true
operating system: Linux
operating system: Mac
primary contact: Matthew McCoy

SNPector
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0208
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3303
citation: https://doi.org/10.1101/834580
description: SNP inspection tool for diagnosing gene pathogenicity and drug response in a naked sequence.
feature list: operation_0331
feature list: operation_0484
feature list: operation 3661

SNPnotes
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 2885
application sub category: topic 3173
application sub category: topic 3517
application sub category: topic 3673
citation: F1000RESEARCH.20415.1
description: high-throughput tissue-specific functional annotation of single nucleotide variants. Tissue-specific variant annotation pipeline. This pipeline annotates variants based on multiple sources of prior knowledge, including the GWAS literature, tissue-specific open chromatin, tissue-specific modulation of gene expression, and clinical pathogenicity. To download and prepare annotation files
feature list: operation 3196
feature list: operation 3226
feature list: operation 3227
feature list: operation 3778

SNPs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3518
citation: https://doi.org/10.1101/725242
description: Genome-wide analysis of polymorphisms identified domestication-associated polymorphism desert carrying important rice grain size/weight QTL | By using SNP-Seek, you abide by the data use license stated | Query for SNPs from the 3000 genome project | - Mansueto, et al. Rice SNP-seek database update: new SNPs, indels, and queries . Nucl. Acids Res. (2017) 45 (D1): D1075-D1081. doi: 10.1093/nar/gkw1135 This paper describes new features and datasets added to SNP-Seek in 2015-2017 as well as software and database updates | This site provides Genotype, Phenotype, and Variety Information for rice (Oryza sativa L.)
feature list: operation_0484
feature list: operation 3196
feature list: operation 3661

SNiPlay
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0102
application sub category: topic_0194
application sub category: topic_0610
application sub category: topic 2885
citation: https://doi.org/10.1101/864504
description: Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data. SNiPlay is a web_based tool for SNP analysis: SNP detection, haplotype reconstruction, diversity analysis and linkage disequilibrium. SNiPloid assumes that short reads datasets (i.e. samples) derived from distinct accessions (diploid or polyploid) have been separately preprocessed as described here.
feature list: operation_0484
feature list: operation_0487
feature list: operation 3196
feature list: operation 3219

SOLQC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0632
application sub category: topic 3068
application sub category: topic 3168
application sub category: topic 3895
citation: https://doi.org/10.1101/840231
description: Synthetic Oligo Library Quality Control Tool. SOLQC - Synthetic Oligo Quality Control tool. SOLQC is a novel analysis tool, which enables fast and comprehensive analysis of synthetic oligo libraries enabling the user comprehensive information and insights about the quality and state of the library
feature list: operation 2428
feature list: operation 3435

SOLart
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0130
application sub category: topic 3474
citation: BTZ773
citation: pubmed:31603466
description: SOLart is a fast and accurate method for predicting the protein solubility of a target protein whose experimental or modeled structure is available. It yields a scaled solubility score with values close to zero indicating aggregate-prone proteins, while values close to 130 designate soluble proteins.
feature list: operation_0409
feature list: operation 3436

SOM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
citation: btu849
citation: pubmed:25543048
description: Python library implementing the full self-organizing map (SOM) analysis workflow.
feature list: operation 2476
feature list: operation 3454
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: http://nbviewer.ipython.org/gist/bougui505/9952997
software help: http://nbviewer.ipython.org/gist/bougui505/9955459
primary contact: Guillaume Bouvier
primary contact: Michael Nilges

SONATA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 3304
application sub category: topic 3306
citation: https://doi.org/10.1101/625491
description: Scalable Open Network Architecture TemplAte (SONATA) Data Format for Efficient Description of Large-Scale Network Models.
feature list: operation 3435
feature list: operation 3450
feature list: operation 3660
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: SONATA DEVELOPER GUIDE.md
primary contact: Anton Arkhipov

SORA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic 3316
application sub category: topic 3673
citation: S40246-019-0227-1
citation: pmcid:PMC6805285
citation: pubmed:31639049
description: Using Apache Spark on genome assembly for scalable overlap-graph reduction. Scalable Overlap-Graph Reduction Algorithms for Genome Assembly using Apache Spark on Cloud. Please go to the Wiki pages, https://github.com/BioHPC/SORA/wiki, to learn about SORA
feature list: operation_0524
feature list: operation_0525
feature list: operation 3216
license: GPL-3.0
software help: wiki

SPAG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3056
application sub category: topic 3673
citation: https://doi.org/10.1101/2019.12.20.884114
description: SPAG is a tool for predicting the spatial distribution of adaptive genetic variants under future climatic conditions.
feature list: operation 3196
feature list: operation 3227
feature list: operation 3891

SPARK-MSNA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0097
application sub category: topic 3170
application sub category: topic 3474
citation: S41598-019-42966-5
citation: pmcid:PMC6488671
citation: pubmed:31036850
description: Efficient algorithm on Apache Spark for aligning multiple similar DNA/RNA sequences with supervised learning.
feature list: operation_0323
feature list: operation_0491
feature list: operation_0492
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0001-6445-7833

SPARQL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0091
application sub category: topic_0621
citation: F1000RESEARCH.21027.1
description: A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3432

SPARSim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
citation: BTZ752
citation: pubmed:31598633
description: SPARSim is a count data simulator for scRNA-seq data.
feature list: operation 2426
feature list: operation 2429
feature list: operation 3799

SPAligner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 3174
citation: https://doi.org/10.1101/744755
description: > HOMEPAGE MISSING! | Alignment of Long Diverged Molecular Sequences to Assembly Graphs | A bstract Background Graph-based representation of genome assemblies has been recently used in different applications from gene finding to haplotype separation. While most of these applications are based on the alignment of molecular sequences to assembly graphs, existing software tools for finding such alignments have important limitations. Results We present a novel SPAligner tool for aligning long diverged molecular sequences to assembly graphs and demonstrate that SPAligner is an efficient solution for mapping third generation sequencing data and can also facilitate the identification of known genes in complex metagenomic datasets. Conclusions Our work will facilitate accelerating the development of graph-based approaches in solving sequence to genome assembly alignment problem
feature list: operation_0523
feature list: operation_0524
feature list: operation_0525

SPCI
type: SoftwareApplication
input: Drug structure
  type: FormalParameter
  additional type: data 2851
  encoding format: format 3814
output: Drug report
  type: FormalParameter
  additional type: data 1696
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 3314
citation: minf.201300029
citation: acs.jcim.6b00371
citation: pubmed:27419846
citation: pubmed:27480236
description: Structural and physico-chemical interpretation of QSAR models
feature list: operation 2426
feature list: operation 2428
is accessible for free: true
operating system: Linux
operating system: Windows
software help: spci-manual.pdf
primary contact: https://orcid.org/0000-0001-5088-8149

SPDI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic 3120
application sub category: topic 3168
citation: btz856
citation: pmcid:PMC7523648
citation: pubmed:31738401
description: Data Model for Variants and Applications at NCBI.
feature list: operation_0525
feature list: operation 3197
feature list: operation 3436

SPDRank
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0209
application sub category: topic 3070
application sub category: topic 3373
citation: J.JMGM.2019.07.009
citation: pubmed:31377536
description: Learning-to-rank technique based on ignoring meaningless ranking orders between compounds | SPDRank is stochastic pairwise descent RankSVM method with ignoring meaningless ranking orders that used on Learning-to-Rank Technique based on Ignoring Meaningless Ranking Orders between Compounds
feature list: operation_0482
license: MIT

SPECTRUM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic 3520
citation: S41598-019-47724-1
citation: pmcid:PMC6677810
citation: pubmed:31375721
description: A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data | Top-Down Proteomics (TDP) is an emerging proteomics protocol that involves identification, characterization, and quantitation of intact proteins using high-resolution mass spectrometry
feature list: operation 3644
feature list: operation 3645
feature list: operation 3860
license: GPL-3.0

SPHARM-PDM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0634
application sub category: topic_0769
application sub category: topic 3384
citation: https://doi.org/10.1117/12.2503894
citation: pmcid:PMC6498854
citation: pubmed:31057203
description: Tool that computes point-based models using a parametric boundary description for the computing of Shape analysis.
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: UNC SPHARM-PDM Tutorial

SPIEC-EASI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic 2269
application sub category: topic 3174
application sub category: topic 3697
citation: https://doi.org/10.1101/2019.12.21.885889
description: Disentangling microbial associations from hidden environmental and technical factors via latent graphical models.
feature list: operation 2495
feature list: operation 3625
feature list: operation 3891

SPINE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0632
application sub category: topic_0736
application sub category: topic_0798
application sub category: topic 3168
citation: gkz1110
citation: pmcid:PMC6954442
citation: pubmed:31745561
description: Targeted insertional mutagenesis libraries for deep domain insertion profiling. SPINE: Saturated Programmable INsertion Engineering. Protein domain insertion via programmed oligo libraries
feature list: operation_0284
feature list: operation_0303
feature list: operation_0308
license: MIT

SPLATCHE3
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0199
application sub category: topic_0654
application sub category: topic 3056
citation: btz311
citation: pmcid:PMC6821363
citation: pubmed:31077292
description: Simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal.
feature list: operation 2426
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: SPLATCHE3 User Manual.pdf
software help: faq3
primary contact: Mathias Currat

SPM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3384
application sub category: topic 3444
citation: pubmed:266227768
description: Statistical Parametric Mapping (SPM) software for the analysis of brain imaging data sequences.
feature list: operation 3435
feature list: operation 3629
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: manual.pdf

SPOT-RNA
type: SoftwareApplication
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1929
output: RNA secondary structure
  type: FormalParameter
  additional type: data_0880
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0097
citation: s41467-019-13395-9
citation: pmcid:PMC6881452
citation: pubmed:31776342
description: RNA secondary structure predictor
feature list: operation_0278
is accessible for free: true
operating system: Linux
software help: README.md
primary contact: https://orcid.org/0000-0002-0478-5533

SPROF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0123
application sub category: topic_0130
application sub category: topic 3382
application sub category: topic 3474
citation: ACS.JCIM.9B00438
citation: pubmed:31800243
description: To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map. Protein sequence profile prediction aims to generate multiple sequences from structural information to advance the protein design. Protein sequence profile can be computationally predicted by energy-based method or fragment-based methods. By integrating these methods with neural networks, our previous method, SPIN2 has achieved a sequence recovery rate of 34%. However, SPIN2 employed only one dimensional (1D) structural properties that are not sufficient to represent 3D structures. In this study, we represented 3D structures by 2D maps of pairwise residue distances. and developed a new method (SPROF) to predict protein sequence profile based on an image captioning learning frame. To our best knowledge, this is the first method to employ 2D distance map for predicting protein properties.
feature list: operation_0272
feature list: operation_0303
feature list: operation_0474
feature list: operation 2492
feature list: operation 2575
license: MIT

SPROUTS
type: SoftwareApplication
input: PDB ID
  type: FormalParameter
  additional type: data 1127
  encoding format: format 1476
input: Mutation ID
  type: FormalParameter
  additional type: data 2209
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
citation: bams-2014-0015
description: SPROUTS has two general functions. The first is to provide existing mutation data given a protein specified by a PDB ID. This is Query mode. The second is to generate new mutation data based on a new PDB ID or a user input. This is Submit mode.
feature list: operation_0224
software version: 1.0

SPUTNIK
type: SoftwareApplication
input: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3579
  encoding format: format 3591
  encoding format: format 3592
  encoding format: format 3603
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3682
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3682
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3382
application sub category: topic 3520
citation: bty622
citation: pmcid:PMC6298046
citation: pubmed:30010780
description: R package for filtering of spatially related peaks in mass spectrometry imaging data.
feature list: operation 3215
feature list: operation 3695
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Paolo Inglese

SPar-K
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3068
application sub category: topic 3169
citation: BTZ416
citation: pubmed:31116370
description: SPar-K (Signal Partitioning using K-means) is a modified version of a standard K-means algorithm designed to cluster vectors containing a sequence of signal (that is, the order in which the elements appear in the vectors is meaningful). In order to detect a possible phase shift or orientation inversion between two vectors, this program allows computing distances between two vectors by shifting and flipping them.
feature list: operation 3501
feature list: operation 3798
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Philipp Bucher
primary contact: Romain Groux

SParQ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0078
application sub category: topic 2229
application sub category: topic 3382
citation: https://doi.org/10.1080/15548627.2019.1695400
citation: pmcid:PMC8386606
citation: pubmed:31752589
description: Streamlined particle quantification (SParQ) plug-in is an automated fluorescent vesicle quantification plug-in for particle quantification in Fiji/ImageJ.
feature list: operation 3454
feature list: operation 3458
feature list: operation 3799

SPeDE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3174
application sub category: topic 3520
application sub category: topic 3697
citation: MSYSTEMS.00437-19
citation: pmcid:PMC6739102
citation: pubmed:31506264
description: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data | A python application for MALDI-TOF MS dereplication | python SPeDE.py <Path\to\ppmc_interval_index.csv> <Project_directory> <Output_directory> [-d <density>] [-c <cluster>] [-l <local>] [-m <cutoff>] [ -o <output_format>\] [-p <peak-count>] [-n <name>] [-q <validation_name>] [-v] [-e] | Command driven processing (Windows and Linux supported, MacOS unknown) | This program cannot be run on a Linux subsystem in Windows
feature list: operation 3627
feature list: operation 3637
feature list: operation 3860
license: MIT

SProCoP
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 2330
input: Peptide identification
  type: FormalParameter
  additional type: data_0945
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: SProCoP is a set of statistical process control aids for visualize, detect, and identify of assignable causes of variation in chromatographic performance (e.g., retention time reproducibility, peak asymmetry, and resolution); and mass spectrometric performance (targeted peptide ion intensity and mass measurement accuracy for high resolving power instruments) via control charts and boxplots.
feature list: operation_0337
feature list: operation 2238

SRH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0194
application sub category: topic 3293
citation: evz193
citation: pmcid:PMC6893154
citation: pubmed:31536115
description: The Prevalence and Impact of Model Violations in Phylogenetic Analysis | tests of stationarity, reversibility, and homogeneity for sequence alignments | This just deletes (with rm -rf, so be careful), /data/srh/processed_data/SRH_tables/ and /data/srh/processed_data/IQtree/ | All scripts have hard-coded input and output destinations. If you want to run them for yourself, you will need to adjust these destinations in each script as you go | This will calculate SRH stats and IQtree input files for all datasets in SRHtests/datasets. It requires python 3.6.x or higher and dependencies as in the header of srh.py. Input and output files are hardcoded near the end of the script, change them if you need to. This script creates two output folders, each of which contains one folder for each dataset in SRHtests/datasets
feature list: operation_0325
feature list: operation_0551
feature list: operation 3478

SSASU
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3382
citation: btz674
citation: pmcid:PMC7523684
citation: pubmed:31504202
description: > MEDIUM CONFIDENCE! | Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs | Semi-blind Sparse Affine Spectral Unmixing (SSASU) for autofluorescence-contaminated micrographs | Semi-blind Sparse Affine Spectral Unmixing (SSASU) | Spectral unmixing methods attempt to determine the concentrations of different fluorophores present at each pixel location in an image by analyzing a set of measured emission spectra

SSEThread
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0611
application sub category: topic 2828
application sub category: topic 3306
citation: J.PBIOMOLBIO.2019.09.003
citation: pmcid:PMC6903780
citation: pubmed:31570166
description: SSEThread is an Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. X-ray crystallography and electron microscopy maps resolved to 3-8 Å are generally sufficient for tracing the path of the polypeptide chain in space, while often insufficient for unambiguously registering the sequence on the path (i.e., threading). Frequently, however, additional information is available from other biophysical experiments, physical principles, statistical analyses, and other prior models. Here, we formulate an integrative approach for sequence assignment to a partial backbone model as an optimization problem, which requires three main components: the representation of the system, the scoring function, and the optimization method.
feature list: operation_0302
feature list: operation_0320
feature list: operation_0479

SSIPe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic_0199
application sub category: topic 3318
citation: btz926
citation: pmcid:PMC7178439
citation: pubmed:31830252
description: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. binding affinity change estimation. SSIPe is a method to calculate binding affinity changes (ΔΔGbind) of protein-protein interactions (PPIs) upon mutations at protein-protein interface. Please direct questions and inquiries to our Service System Discussion Board or contact Dr. Estimation of binding affinity change upon mutations at protein-protein interface
feature list: operation 2464
feature list: operation 2492
feature list: operation 2495
license: MIT

SSNpipe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0160
application sub category: topic_0821
application sub category: topic 3293
citation: JBC.RA119.010619
citation: pmcid:PMC6827312
citation: pubmed:31501245
description: A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16) | a GUI to Simplify the Generation of Sequence Similarity Networks | SSNpipe is a Python program, and independent all-inclusive executable binary files for most popular operating systems are freely available in release page | Please be aware that SSNpipe and all python Tkinter applications are unable to run on MacOS Mojave 10.14.6, due to an unidentified bug in the MacOS system. This issue should be patched in the soon to be released MacOS Catalina 10.15, click here for more information)
license: GPL-3.0

SSRSC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3168
application sub category: topic 3318
application sub category: topic 3382
citation: TCYB.2019.2943691
citation: pubmed:31634148
description: Scaled Simplex Representation for Subspace Clustering.
feature list: operation 2939
feature list: operation 3432
feature list: operation 3659

SSnet
type: SoftwareApplication
input: Protein features
  type: FormalParameter
  additional type: data 1277
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic 2275
application sub category: topic 3336
application sub category: topic 3474
application sub category: topic 3542
citation: https://doi.org/10.1101/2019.12.20.884841
description: Secondary Structure based End-to-End Learning model for Protein-Ligand Interaction Prediction. Abstract Computational prediction of bioactivity has become a critical aspect of modern drug discovery as it mitigates the cost, time, and resources required to find and screen new compounds. Deep Neural Networks (DNN) have recently shown excellent performance in modeling Protein-Ligand Interaction (PLI). However, DNNs are only effective when physically sound descriptions of ligands and proteins are fed into the network for further processing. Furthermore, previous research has not incorporated the secondary structure of the protein in a meaningful manner. In this work, we utilize secondary structure information of the protein which is extracted as the curvature and torsion of the backbone of protein to predict PLI. https://github.com/ekraka/SSnet
feature list: operation 2423
software help: SSnet
software version: 1.0
primary contact: 0000-0003-4762-944X

ST-SIM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3361
application sub category: topic 3489
citation: TOH.2019.2962446
citation: pubmed:31880560
description: Subjective Evaluation of the Spectral Temporal SIMilarity (ST-SIM) Measure for Vibrotactile Quality Assessment. Recent standardization efforts for Tactile Internet (TI) and haptic codecs have paved the route for delivering tactile experiences in synchrony with audio and visual interaction components. Since humans are the ultimate consumers of tactile interactions, it is utmost important to develop objective quality assessment measures that are in close agreements with human perception. In this work, we present the results of a large-scale subjective study of a recently proposed objective quality assessment approach for vibrotactile signals called ST-SIM (Spectral Temporal SIMilarity). ST-SIM encompasses two components: perceptual spectral and temporal similarity measures. Two subjective experiments were conducted to validate ST-SIM, and elicited subjective ratings are used to create a VibroTactile Quality Assessment (VTQA) database.
feature list: operation 2428
feature list: operation 3435

HGGM-LIM Split-Bregman-ST-Total-Variation-MRI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3304
application sub category: topic 3444
description: 2D and 3D constrained Total Variation using the Split Bregman formulation
feature list: operation 3359
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.1.0.0
primary contact: Juan Felipe Pérez Juste Abascal

STAFF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3382
application sub category: topic 3398
citation: https://doi.org/10.3791/60493
citation: pubmed:31789313
description: Spatial Temporal Analysis of Fieldwise Flow in Microvasculature. Changes in blood flow velocity and distribution are vital in maintaining tissue and organ perfusion in response to varying cellular needs. Further, appearance of defects in microcirculation can be a primary indicator in the development of multiple pathologies. Advances in optical imaging have made intravital microscopy (IVM) a practical approach, permitting imaging at the cellular and subcellular level in live animals at high-speed over time. Yet, despite the importance of maintaining adequate tissue perfusion, spatial and temporal variability in capillary flow is seldom documented. In the standard approach, a small number of capillary segments are chosen for imaging over a limited time. To comprehensively quantify capillary flow in an unbiased way we developed Spatial Temporal Analysis of Fieldwise Flow (STAFF), a macro for FIJI open-source image analysis software
feature list: operation 3435
feature list: operation 3443
feature list: operation 3799
software help: STAFF User Guide v1.pdf

START-R
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0605
application sub category: topic_0654
application sub category: topic 3173
application sub category: topic 3518
citation: https://doi.org/10.1101/858803
description: New, easy, quick and efficient DNA replication timing analysis by high-throughput approaches. Simple Tool for Analysis of Replication Timing with R. Visit our website : https://thomasdenecker.github.io/START-R/. We use Docker to develop and manage START-R. We invite you to verify that the following requirements are correctly satisfied before trying to bootstrap the application:
feature list: operation 3192
license: BSD-3-Clause

STEM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3305
application sub category: topic 3324
application sub category: topic 3395
citation: HS.2019.0018
citation: pmcid:PMC6708268
citation: pubmed:31433284
description: An Open Source Tool for Disease Modeling | The Eclipse Foundation - home to a global community, the Eclipse IDE, Jakarta EE and over 350 open source projects, including runtimes, tools and frameworks | The Spatiotemporal Epidemiological Modeler (STEM) Project | Some Eclipse Foundation pages use cookies to better serve you when you return to the site. You can set your browser to notify you before you receive a cookie or turn off cookies. If you do so, however, some areas of some sites may not function properly. To read Eclipse Foundation Privacy Policy click here | The Spatiotemporal Epidemiological Modeler (STEM) tool is designed to help scientists and public health officials create and use spatial and temporal models of emerging infectious diseases. These models can aid in understanding and potentially preventing the spread of such diseases
feature list: operation 2426

STRmix
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0625
application sub category: topic 2885
citation: https://doi.org/10.1111/1556-4029.13898
citation: pubmed:30132900
description: Probabilistic genotyping software that combines biological modelling and mathematical processes to interpret a wide range of complex DNA profiles.
feature list: operation 2428
feature list: operation 3196
feature list: operation 3629
is accessible for free: false
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Vic Meles

STS-NLSP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 3336
application sub category: topic 3375
citation: FBIOE.2019.00306
citation: pmcid:PMC6851049
citation: pubmed:31781551
description: A Network-Based Label Space Partition Method for Predicting the Specificity of Membrane Transporter Substrates Using a Hybrid Feature of Structural and Semantic Similarity. codes for the membrane transporter paper. codes for membrane transporter paper:. model_training_*.py are codes for parameter tuning in a server
feature list: operation 2871
feature list: operation 2929
feature list: operation 3454

ST viewer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3308
application sub category: topic 3382
application sub category: topic 3518
citation: bty714
citation: pubmed:30875427
description: Tool for analysis and visualization of spatial transcriptomics datasets.
feature list: operation 3798
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: wiki
primary contact: Jose Fernandez Navarro

STing
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic 3168
application sub category: topic 3305
application sub category: topic 3489
citation: https://doi.org/10.1101/855478
description: accurate and ultrafast genomic profiling with exact sequence matches. Ultrafast sequence typing and gene detection from NGS raw reads. See the full documentation at: https://sting.readthedocs.io/
feature list: operation 3211
feature list: operation 3227
feature list: operation 3472
feature list: operation 3482
feature list: operation 3840

SURFY
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3475
output: Heat map
  type: FormalParameter
  additional type: data 1636
  encoding format: format 3603
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0140
citation: pnas.1808790115
citation: pmcid:PMC6243280
citation: pubmed:30373828
description: Visualize the human surface proteome (surfaceome) and load your own expression data to inspect and uncover cellular phenotypes and new surfaceome markers.
feature list: operation 2489
feature list: operation 2942
operating system: Linux
operating system: Mac
operating system: Windows

SURVTOOLS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3302
application sub category: topic 3305
application sub category: topic 3500
citation: J.EXPPARA.2019.107808
citation: pubmed:31765613
description: Risk-based surveillance for meat-borne parasites. There is a plethora of meat-borne hazards - including parasites - for which there may be a need for surveillance. However, veterinary services worldwide need to decide how to use their scarce resources and prioritise among the perceived hazards. Moreover, to remain competitive, food business operators - irrespective of whether they are farmers or abattoir operators - are preoccupied with maintaining a profit and minimizing costs. Still, customers and trade partners expect that meat products placed on the market are safe to consume and should not bear any risks of causing disease. Risk-based surveillance systems may offer a solution to this challenge by applying risk analysis principles; first to set priorities, and secondly to allocate resources effectively and efficiently.

SUSPECT-BDQ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0199
application sub category: topic 3474
citation: JOURNAL.PONE.0217169
citation: pmcid:PMC6541270
citation: pubmed:31141524
description: StrUctural Susceptibility PrEdiCTion on BDQ.
feature list: operation_0331
feature list: operation_0478
feature list: operation 3202
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: David B. Ascher

SVCA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 2269
application sub category: topic 2640
application sub category: topic 3300
application sub category: topic 3382
citation: j.celrep.2019.08.077
citation: pmcid:PMC6899515
citation: pubmed:31577949
description: Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis. Spatial Variance Components Analysis (SVCA). NB: If you are already a limix user, we recommend you install svca_limix and svca in a dedicated conda environment so there is no interference between your limix versions
feature list: operation_0313
feature list: operation 2436
feature list: operation 3891
license: Apache-2.0

SVJedi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0625
application sub category: topic 3168
application sub category: topic 3175
citation: https://doi.org/10.1101/849208
description: Genotyping structural variations with long reads. SVJedi : Genotyping structural variations with long read data. SVJedi is a structural variation (SV) genotyper for long read data. Based on a representation of the different alleles, it estimates the genotype of each variant in a given individual sample based on allele-specific alignment counts. SVJedi takes as input a variant file (VCF), a reference genome (fasta) and a long read file (fasta/fastq) and outputs the initial variant file with an additional column containing genotyping information (VCF)
feature list: operation_0484
feature list: operation 3196
feature list: operation 3198
feature list: operation 3227
license: AGPL-3.0

SVScore
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2885
application sub category: topic 3175
application sub category: topic 3512
citation: btw789
citation: pmcid:PMC5408916
citation: pubmed:28031184
description: Impact prediction tool for structural variation.
feature list: operation_0484
feature list: operation 3436
feature list: operation 3461
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Ira M. Hall

SVants
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0798
application sub category: topic 3175
application sub category: topic 3500
citation: https://doi.org/10.1101/822312
description: SVants – A long-read based method for structural variation detection in bacterial genomes. Config file input files and parameters. Output from LastalAlignToGenome.sh. git clone https://github.com/EpiBlake/SVants.git
feature list: operation_0525
feature list: operation 3198
feature list: operation 3228
license: GPL-3.0

SVs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0114
application sub category: topic_0196
application sub category: topic 3170
application sub category: topic 3303
citation: S13059-019-1828-7
citation: pmcid:PMC6868818
citation: pubmed:31747936
description: Genome-wide Reconstruction of Complex Structural Variants, or GROC-SVs, is a software pipeline for identifying large-scale structural variants, performing sequence assembly at the breakpoints, and reconstructing the complex structural variants using the long-fragment information from the 10x Genomics platform.
feature list: operation_0524
feature list: operation 2429
feature list: operation 3192
feature list: operation 3216
feature list: operation 3227
license: MIT

SW-Tandem
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: btz147
description: Tool for large-scale peptide identification with parallel spectrum dot product on Sunway TaihuLight.
feature list: operation 3431
feature list: operation 3646
is accessible for free: true
license: Unlicense
operating system: Linux
software help: README.md

SWAPCounter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic 3168
application sub category: topic 3316
citation: S12539-019-00348-5
citation: pubmed:31734873
description: Counting Kmers for Biological Sequences at Large Scale. This is a distributed kmer counting tools for TB-PB sequencing dataset
feature list: operation_0524
feature list: operation 3472
feature list: operation 3695

SWPepNovo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 3520
application sub category: topic 3673
citation: IJBS.32142
citation: pmcid:PMC6743289
citation: pubmed:31523183
description: An Efficient De Novo Peptide Sequencing Tool for Large-scale MS/MS Spectra Analysis | Introduction： As the number of the MS/MS spectra increases rapidly, the excessive computation time taken by MS/MS spectra data analysis has become a critical concern in computational biology. In this work, we designed and implemented SWPepNovo, an efficient de novo peptide sequencing tool for large-scale MS/MS spectra data analysis using a novel peptide-spectrum matches (PSMs) algorithm. To achieve the high performance, we designed an improved scoring algorithm to reduce the time complexity and eliminate the data dependence to enable all possible locality and vectorizations. Performance is also tuned by pre-fetching, double buffering mechanism, and an optimized memory access scheme, to achieve an optimum performance and best utilization of various computing resources within neo-heterogeneous many-core architecture
feature list: operation 3202
feature list: operation 3644
feature list: operation 3646

SWiFi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0593
application sub category: topic 3047
citation: J.BPJ.2019.10.033
citation: pmcid:PMC6895709
citation: pubmed:31711608
description: Confinement-Free Wide-Field Ratiometric Tracking of Single Fluorescent Molecules. A software for single particle tracking which includes intensity ratiometric measurements and analysis. Unpack the zip file to a folder of your choice. follow the instructions in the manual in order to get started
feature list: operation_0337
feature list: operation 3457
feature list: operation 3891
license: GPL-3.0

SZN Zoological Collection Database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3500
description: Database containing 4.373 video, 18.212 still images and 7.771 labels concerning sampled that were prepared and stored from 1910 at the “Stazione Zoologica Anton Dohrn di Napoli (SZN)”. Moreover, the digitised version of 38 documents (totalling 8406 pages) with important information about taxonomy, ecology and phylogenetic is also included.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

Sage
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
input: Mass spectrum
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3244
output: Peptide identification
  type: FormalParameter
  additional type: data_0945
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: acs.jproteome.3c00486
citation: pubmed:37819886
description: Sage is a proteomics database search engine to match tandem mass spectra to peptides. Sage also performs retention time prediction, quantificaiton and FDR control.
feature list: operation 2428
feature list: operation 3631
feature list: operation 3633
license: MIT
software help: docs

SalMotifDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic_0749
citation: S12864-019-6051-0
citation: pmcid:PMC6720087
citation: pubmed:31477007
description: a tool for analyzing putative transcription factor binding sites in salmonid genomes | SalMotifDB: cis-regulatory motif database for salmonids | We're getting there, it's worth the wait
feature list: operation_0441
feature list: operation_0445
feature list: operation 3439

SamPler
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic 3407
citation: S12859-019-3038-4
citation: pmcid:PMC6727554
citation: pubmed:31488049
description: > MEDIUM CONFIDENCE! | a novel method for selecting parameters for gene functional annotation routines | Novel strategy for selecting best parameters for gene functional annotation routines in merlin | readme instructions updated · 81b3a5a9
feature list: operation_0495
feature list: operation 1812
feature list: operation 2422

SanXoT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic 3520
citation: bty815
citation: pmcid:PMC6499250
citation: pubmed:30252043
description: Modular and versatile package for the quantitative analysis of high-throughput proteomics experiments.
feature list: operation 3799
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: How to use SanXoT
primary contact: E. Bonzon-Kulichenko
primary contact: Jesús María Vázquez Cobos

SavvyCNV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0632
application sub category: topic 3676
citation: https://doi.org/10.1101/617605
description: Genome-wide copy number variants (CNV) calling from off-target reads.
feature list: operation 3196
feature list: operation 3227
feature list: operation 3435
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Matthew N. Wakeling

ScType
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3489
citation: https://doi.org/10.1101/812131
description: ScType is a tool for fully-automated cell type identification from single-cell RNA-seq data. ScType provides a complete pipeline for single-cell RNA-seq data analysis (including data processing, normalization and clustering) and cell-type annotation.
feature list: operation 3432
feature list: operation 3435
feature list: operation 3680

Scallop-LR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: https://doi.org/10.1101/632703
description: Accurate reference-based transcript assembler.
feature list: operation_0264
feature list: operation 3258
feature list: operation 3798
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Carl Kingsford

Scan
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0091
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic 3308
description: Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data
feature list: operation 2437
feature list: operation 3792
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Scan
software version: 1.0

ScanFold
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0097
application sub category: topic_0099
application sub category: topic_0160
application sub category: topic_0166
application sub category: topic_0622
citation: j.ymeth.2019.11.001
citation: pmcid:PMC7205576
citation: pubmed:31711930
description: Mapping the RNA structural landscape of viral genomes. ScanFold is an RNA sequence scanning pipeline which attempts to identify potentially functional RNA secondary structures. This is done by first scanning a single input sequence to identify regions which generate negative thermodynamic z-scores (a hallmark of functional RNA sequences), and subsequently identifying the specific base pairs which we…. Welcome to the ScanFold web server. Using the ScanFold web server you can identify regions of an RNA sequence which generate unusually stable secondary structures (one of the hallmarks of a functional RNA)
feature list: operation_0238
feature list: operation_0502
feature list: operation 2441

ScanITD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: ScanITD: detecting internal tandem duplication with robust variant allele frequency estimation
feature list: operation 3963

Scavenger
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0769
application sub category: topic 3170
citation: F1000RESEARCH.19426.1
description: A pipeline for recovery of unaligned reads utilising similarity with aligned reads | Rescue potential false negative unmapped reads in alignment tools | Manuscript available now on bioRxiv: https://www.biorxiv.org/content/early/2018/06/13/345876 | python3 usage: scavenger.py [options] -G/--genome_file <genome_file> -i/--input -at/--aligner_tool <aligner>
feature list: operation 3198
feature list: operation 3227
feature list: operation 3798
license: MIT

Sci-Hub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3068
application sub category: topic 3382
application sub category: topic 3489
citation: PEERJ.PREPRINTS.3100V3
citation: pmcid:PMC5832410
citation: pubmed:29424689
description: Sci-Hub provides access to nearly all scholarly literature. Source code and data analyses for the Sci-Hub Coverage Study. Analyses for the Sci-Hub Coverage Study. Manuscript for the Sci-Hub Coverage Study. Manuscript source for the Sci-Hub Coverage Study. Data for the Sci-Hub Stats Browser. removing barriers in the way of science. Din bedste informationskilde om sci hub. This project investigates the coverage of scholarly literature in the Sci-Hub and LibGen scimag repositories. It's based on using DOIs to uniquely identify articles. For more information, see the corresponding study:. This is the manuscript source for the study titled Sci-Hub provides access to nearly all scholarly literature. Sci-Hub is a pirate website that provides access to full texts from the scholarly literature, including paywalled articles. The first pirate website in the world to open mass and public access to tens of millions research papers
feature list: operation_0306
feature list: operation_0337
feature list: operation 3431

Sci-LMM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3053
application sub category: topic 3305
application sub category: topic 3810
citation: JOURNAL.PGEN.1008124
citation: pmcid:PMC6529016
citation: pubmed:31071088
description: Modeling framework for studying population-scale family trees that combines techniques from the animal and plant breeding literature and from human genetics literature.
feature list: operation 3196
feature list: operation 3659
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0003-1432-7461

SciApps
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3169
application sub category: topic 3170
citation: https://doi.org/10.1101/852269
description: A Cloud-Based Platform for Analyses and Distribution of the MaizeCODE data. MaizeCODE is a project aimed at identifying and analyzing functional elements in the maize genome. In its initial phase, MaizeCODE assayed up to five tissues from four maize strains (B73, NC350, W22, TIL11) by RNA-Seq, Chip-Seq, RAMPAGE, and small RNA sequencing. To facilitate reproducible science and provide both human and machine access to the MaizeCODE data, we developed SciApps, a cloud-based portal, for analysis and distribution of both raw data and analysis results. Based on the SciApps workflow platform, we generated new components to support the complete cycle of the MaizeCODE data management
feature list: operation 2422
feature list: operation 3208
feature list: operation 3454

Scientific Educational
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0632
application sub category: topic 3293
application sub category: topic 3297
citation: VETWORLD.2019.959-964
citation: pmcid:PMC6702558
citation: pubmed:31528018
description: Sequence analysis of the cytochrome c oxidase subunit 1 gene of Sarcoptes scabiei isolated from goats and rabbits in East Java, Indonesia | Software for the Molecular Biologist | Welcome to the Sci Ed Software website
feature list: operation_0308
feature list: operation 3200
feature list: operation 3891

ScisTree
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0625
application sub category: topic 2229
citation: https://doi.org/10.1101/742395
description: Accurate and Efficient Cell Lineage Tree Inference from Noisy Single Cell Data | Cell tree inference and genotype calling from noisy single cell data | ScisTree is a computer program for inferring cell tree and calling genotypes from uncertain single cell genotype data. If you use ScisTree, please cite: | The key feature of ScisTree is that it works with uncertain genotypes with individualized probability. That is, you can specify for each genotype (at a row/cell or column/site) different probabilities of being a particular genotype state. ScisTree allows both binary or ternary genotypes. Here is an example for binary genotypes. Note: don't include blank rows in the input genotype file
feature list: operation_0547
feature list: operation 3196
feature list: operation 3557

SeRenDIP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
citation: BTZ428
citation: pubmed:31116381
description: SEquential REmasteriNg to DerIve Profiles for fast and accurate predictions of PPI interface positions.
feature list: operation 2492
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: K. Anton Feenstra
primary contact: Paul de Geest
primary contact: Q. Hou

SecStrAnnotator
type: SoftwareApplication
input: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1475
output: Protein residue
  type: FormalParameter
  additional type: data 1756
  encoding format: format 2077
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic 1317
description: Annotation of secondary structure elements in proteins.
feature list: operation_0226
operating system: Linux
operating system: Mac
operating system: Windows

Seeksv
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3794
citation: btw591
citation: pubmed:27634948
description: Accurate tool for somatic structural variation and virus integration detection.
feature list: operation_0452
feature list: operation 3227
feature list: operation 3228
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Bo Liao

Selene
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3068
application sub category: topic 3071
application sub category: topic 3474
citation: s41592-019-0360-8
citation: pmcid:PMC7148117
citation: pubmed:30923381
description: PyTorch-based deep learning library for sequence data.
feature list: operation 3278
feature list: operation 3279
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorials
software help: faq.html
software help: installation.html
software version: 0.3.1
primary contact: Troyanskaya Laborator

SelfTarget
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 2330
output: Nucleic acid report
  type: FormalParameter
  additional type: data 2084
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic 2269
application sub category: topic 3321
application sub category: topic 3474
citation: nbt.4317
citation: pmcid:PMC6949135
citation: pubmed:30480667
description: Computational predictor of the mutations generated by repair of CRISPR-Cas9-induced double-strand breaks (command line version of FORECasT).
feature list: operation 2238
feature list: operation 2423
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md

Selfish
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3295
citation: BTZ362
citation: pmcid:PMC6612869
citation: pubmed:31510653
description: discovery of differential chromatin interactions via a self-similarity measure | SELFISH (Discovery of Differential Chromatin Interactions via a Self-Similarity Measure) is a tool for finding differential chromatin interactions between two Hi-C contact maps. It uses self-similarity to model interactions in a robust way. For more information read the full paper: Selfish: Discovery of Differential Chromatin Interactions via a Self-Similarity Measure. A Python implementation of Selfish is available at Ay-lab
feature list: operation_0272
feature list: operation 3192
feature list: operation 3501

SeneQuest
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
application sub category: topic 3300
application sub category: topic 3360
citation: J.CELL.2019.10.005
citation: pubmed:31675495
description: SeneQuest contains information on gene-to-senescence associations is crucial for increasing our understanding of the molecular mechanisms driving senescence.

Sentieon DNASeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3168
application sub category: topic 3810
citation: FGENE.2019.00736
citation: pmcid:PMC6710408
citation: pubmed:31481971
description: Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy | As reliable, efficient genome sequencing becomes ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important
feature list: operation 3227

Sentinel-1
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3050
application sub category: topic 3837
citation: S41467-019-12737-X
citation: pmcid:PMC6802221
citation: pubmed:31628336
description: Radar vision in the mapping of forest biodiversity from space.
feature list: operation 2429
feature list: operation 2940
feature list: operation 3435

Sentinel-1 SLC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3810
citation: PREPRINTS201911.0393.V1
description: A Generic Practice for Generating Dual-pol Covariance Matrix Elements in SNAP S-1 Toolbox.
license: GPL-3.0

Seq2Feature
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0199
citation: btz432
citation: pubmed:31135038
description: Web-based feature extraction tool which computes protein and DNA sequence driven features. It can calculate 252 protein- based and 42 DNA- based descriptors.
feature list: operation_0250
feature list: operation_0267
feature list: operation_0455
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Prof. Michael Gromiha

SeqBreed
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3517
citation: https://doi.org/10.1101/748624
description: a python tool to evaluate genomic prediction in complex scenarios | SeqBreed.py is a python3 software to simulate populations under (genomic) selection. It inherits most of funcionality from SBVB (Perez-Enciso et al., 2017, https://github.com/miguelperezenciso/sbvb1) and pSBVB (Zingaretti et al. 2018, https://github.com/lauzingaretti/pSBVB) softwares but code has been completely rewritten. It is now much more user friendly and adds numerous new features such as easy selection implementation (BLUP, GBLUP, SSTEP), plots (PCA, GWAS)..
feature list: operation_0487
feature list: operation 3196
feature list: operation 3891

SeqDivA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0121
application sub category: topic_0160
application sub category: topic_0623
application sub category: topic 3168
citation: biom10010026
citation: pmcid:PMC7022958
citation: pubmed:31878100
description: Graph Theory-Based Sequence Descriptors as Remote Homology Predictors.
feature list: operation_0524
feature list: operation 3092
feature list: operation 3472
license: GPL-3.0

SeqSero2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0622
application sub category: topic 3673
citation: aem.01746-19
citation: pmcid:PMC6856333
citation: pubmed:31540993
description: rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode)
feature list: operation 3182
feature list: operation 3211
feature list: operation 3482
license: GPL-2.0

SeqTailor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
additional type: Web service
application sub category: topic_0199
application sub category: topic_0654
application sub category: topic 3673
citation: GKZ326
citation: pmcid:PMC6602489
citation: pubmed:31045209
description: Web server for the extraction of DNA or protein sequences from next-generation sequencing data.
feature list: operation_0433
feature list: operation 3216
feature list: operation 3227
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation.html
primary contact: 0000-0002-6129-567X

SeqVec
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0218
application sub category: topic_0623
application sub category: topic 3474
citation: S12859-019-3220-8
citation: pmcid:PMC6918593
citation: pubmed:31847804
description: Modeling aspects of the language of life through transfer-learning protein sequences. Modelling the Language of Life - Deep Learning Protein Sequences. Repository for the paper Modeling aspects of the language of life through transfer-learning protein sequences. Holds pre-trained SeqVec model for creating embeddings for amino acid sequences. Also, contains checkpoint for fine-tuning
feature list: operation_0267
feature list: operation_0337
feature list: operation_0477
feature list: operation 2489
feature list: operation 3904
license: MIT

Sequence tube maps
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic 3382
citation: btz597
citation: pmcid:PMC6954646
citation: pubmed:31368484
description: making graph genomes intuitive to commuters | displays multiple genomic sequences in the form of a tube map | A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg | Link to working demo: https://vgteam.github.io/sequenceTubeMap/ | Run Sequence Tube Maps On Your Own | If you are using vg and want visualize the graphs it generates, the online version is limited to small file sizes. For visualizing bigger data sets you can run Sequence Tube Maps on your own. You can either run Tube Maps completely on your local (Linux) machine or use your local browser to access Tube Maps running on any other (Linux) machine you have access to
license: MIT

Sequencing Initiative Suomi (SISu)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 3168
description: The Sequencing Initiative Suomi (SISu) search engine offers a way to search for data on sequence variants in Finns. It provides valuable summary data for researchers and clinicians as well as other people having an interest in genetics in Finland. With SISu, you can examine the attributes and appearance of different variants in Finnish cohorts and see their aggregate distribution in Finland visualized on a map.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
software help: how-to-use
primary contact: Risto Kajanne

SeroCall
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3168
application sub category: topic 3305
application sub category: topic 3418
citation: https://doi.org/10.1101/741603
description: Determining the serotype composition of mixed samples of pneumococcus using whole genome sequencing | Pneumococcal serotype quantification using NGS reads | SeroCall can identify and quantitate the capsular serotypes in Illumina whole-genome sequencing samples of S. pneumoniae, calculating abundances of each serotype in mixed cultures. The software is written in Python (compatible with Python 2 or 3), and is freely available under an open source GPLv3 license
feature list: operation 3798
feature list: operation 3799
license: GPL-3.0

Serosolver
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0804
application sub category: topic 3305
application sub category: topic 3324
citation: https://doi.org/10.1101/730069
description: an open source tool to infer epidemiological and immunological dynamics from serological data | Inference framework for serological data | serosolver is a modelling and inference package that uses a dynamic model to infer antibody dynamics and infection histories from cross-sectional or longitudinal serological data. The model infers individual-level infection histories, historical attack rates, and patterns of antibody dynamics by accounting for cross-reactive antibody responses and measurement error
license: GPL-3.0

Seurat SingleR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/827139
description: Evaluation of Cell Type Deconvolution R Packages on Single Cell RNA-seq Data.
feature list: operation 3435
feature list: operation 3629
feature list: operation 3659

ShNeigh
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3315
citation: https://doi.org/10.1101/741447
description: Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci | [posMatrix,retVals]=ShNeigh(heatmapMatrix,method_type)

ShaKer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0099
application sub category: topic 3474
citation: BTZ395
citation: pmcid:PMC6612843
citation: pubmed:31510707
description: RNA SHAPE prediction using graph kernel | SHApe simulation with graph KERnels | import shaker.rna_tools.rna_io as rio
feature list: operation_0267
feature list: operation_0278
feature list: operation 2441

Shambhala
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3518
citation: s12859-019-2641-8
citation: pmcid:PMC6366102
citation: pubmed:30727942
description: Platform-agnostic data harmonizer for gene expression data.
feature list: operation_0313
feature list: operation_0533
feature list: operation 3431
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

Shark
type: SoftwareApplication
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1930
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
output: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 1930
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
citation: btaa779
citation: https://doi.org/10.1101/836130
description: Fast tool for mapping-free gene separation of reads, using Bloom filter.
feature list: operation 3695
is accessible for free: true
license: GPL-3.0
operating system: Linux
software version: 1.2.0

Shift-T
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0593
application sub category: topic_0632
citation: PRO.3785
citation: pmcid:PMC6933856
citation: pubmed:31730280
description: Shift-T is a server for an automated Variable-Temperature NMR Data Analysis.
feature list: operation_0461
feature list: operation 2476
feature list: operation 3215
license: MIT

ShinyFMBN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3297
description: App developed in Shiny and usable in R environment that allows to visualize, explore, filter and extract data from FoodMicrobionet.
software version: 1.1

ShinyGO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0780
application sub category: topic 3500
citation: btz931
citation: pmcid:PMC7178415
citation: pubmed:31882993
description: ShinyGO is a graphical enrichment tool for animals and plants.
feature list: operation 2422
feature list: operation 2436
feature list: operation 3083

ShinyLearner
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3581
output: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3391
application sub category: topic 3473
citation: https://doi.org/10.1101/675181
description: A software framework for performing benchmarks of machine-learning classification algorithms
feature list: operation 2990
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: ShinyLearner

ShinySOM
type: SoftwareApplication
input: Experimental measurement
  type: FormalParameter
  additional type: data 3108
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0804
application sub category: topic 2229
application sub category: topic 3934
citation: btaa091
citation: pmcid:PMC7214046
citation: pubmed:32049322
description: Precise, high-performance FlowSOM-style cytometry data analysis in a browser, in an R Shiny app.
feature list: operation_0313
feature list: operation_0571
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: TUTORIAL.md
primary contact: http://orcid.org/0000-0001-7356-4075

ShuTu
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0749
application sub category: topic 3382
citation: FNINF.2019.00068
citation: pmcid:PMC6834530
citation: pubmed:31736735
description: ShuTu is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining.
feature list: operation 1812
feature list: operation 3450
feature list: operation 3799

SiCloneFit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0199
application sub category: topic_0625
citation: GR.243121.118
citation: pmcid:PMC6836738
citation: pubmed:31628257
description: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data. Accumulation and selection of somatic mutations in a Darwinian framework result in intra-tumor heterogeneity (ITH) that poses significant challenges to the diagnosis and clinical therapy of cancer. Identification of the tumor cell populations (clones) and reconstruction of their evolutionary relationship can elucidate this heterogeneity. Recently developed single-cell DNA sequencing (SCS) technologies promise to resolve ITH to a single-cell level. However, technical errors in SCS data sets, including false-positives (FP) and false-negatives (FN) due to allelic dropout, and cell doublets, significantly complicate these tasks. Here, we propose a nonparametric Bayesian method that reconstructs the clonal populations as clusters of single cells, genotypes of each clone, and the evolutionary relationship between the clones
feature list: operation 2238
feature list: operation 3196
feature list: operation 3432

SiRJ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic 3474
citation: APL0000468
citation: pubmed:31789550
description: A general response process theory for situational judgment tests. Situational judgment tests (SJTs) have emerged as a staple of assessment methodologies for organizational practitioners and researchers. Despite their prevalence, many questions regarding how to interpret respondent choices or how variations in item construction and instruction influence the nature of observed responses remain. Existing conceptual and empirical efforts to explore these questions have largely been rooted in reflexive psychometric measurement models that describe participant responses as indicative of (usually multiple) latent constructs. However, some have suggested that a key to better understanding SJT responses lies in unpacking the judgment and decision-making processes employed by respondents and the psychological and contextual factors that shape how those processes play out. To this end, the present article advances an integrative and generalizable process-oriented theory of SJT responding

Sierra
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3512
citation: https://doi.org/10.1101/867309
description: Discovery of differential transcript usage from polyA-captured single-cell RNA-seq data. Sierra is an R package designed for detecting differential transcript usage analysis from polyA-enriched single cell RNASeq data. Sierra identifies coordinates of read pileups (i.e. peaks) and performs UMI counting, followed by differential usage analysis between defined cell populations. Please read vignette for a demonstration on how to use this software
feature list: operation 2495
feature list: operation 3222
feature list: operation 3891

SieveSifter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic_0602
application sub category: topic 2830
application sub category: topic 3379
citation: btx168
description: Web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.
feature list: operation_0560
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: data
primary contact: Andrew Fiore-Gartland

SigHotSpotter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic_0749
application sub category: topic 2229
application sub category: topic 3170
citation: btz827
citation: pmcid:PMC7703776
citation: pubmed:31697324
description: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies.
feature list: operation_0277
feature list: operation 2428
feature list: operation 3439

SigProfilerMatrixGenerator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic 3068
application sub category: topic 3676
citation: https://doi.org/10.1101/653097
description: Tool for visualizing and exploring patterns of small mutational events.
feature list: operation_0335
is accessible for free: true
license: BSD-2-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: home
primary contact: Erik Bergstrom

SigUNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0140
application sub category: topic_0154
application sub category: topic_0621
application sub category: topic 3474
application sub category: topic 3510
citation: S12859-019-3245-Z
citation: pmcid:PMC6923836
citation: pubmed:31861981
description: signal peptide recognition based on semantic segmentation. A signal peptide predictor based on deep learning. For CPU: pip3 install -r requirement.cpu.txt. For GPU (suggest): pip3 install -r requirement.gpu.txt
feature list: operation_0277
feature list: operation_0418
feature list: operation 3439

Signaling Pathways Project
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3277
application sub category: topic 3308
citation: S41597-019-0193-4
citation: pmcid:PMC6823428
citation: pubmed:31672983
description: integrated 'omics knowledgebase for mammalian cellular signaling pathways. A multi-omics knowledgebase for cellular signaling pathways. Welcome to the Signaling Pathways Project. The Signaling Pathways Project is a multi-omics knowledgemine based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench relevant to cellular signaling pathways. Learn more ». 1555 datasets found. Use the filter to narrow the listings. Transcriptomic Cistromics (ChIP-Seq)
feature list: operation_0306
feature list: operation_0440
feature list: operation_0533
feature list: operation 3359
feature list: operation 3439
software help: docs

SigsPack
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0130
application sub category: topic_0199
application sub category: topic 2640
citation: S12859-019-3043-7
citation: pmcid:PMC6720940
citation: pubmed:31477009
description: package for cancer mutational signatures | SigsPack R/Bioconductor package for mutational signature estimation | SigsPack provides estimations of a sample's exposure to mutational processes described by a set of known mutational signatures (for example from COSMIC). The exposure stability is quantified by bootstrapping the mutational catalogue
feature list: operation_0337
feature list: operation 3202
feature list: operation 3435

SikuliX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3382
citation: https://doi.org/10.1101/783340
description: Automated Spatially Targeted Optical Micro Proteomics (autoSTOMP) to determine protein complexity of subcellular structures | Automate what you see on a computer monitor | What is it? For what is it? Get it? Use it? Get help? Contribute? | Latest stable version: 2.0.0 —— Nightly builds: 2.1.0-SNAPSHOT | Both left the project at Sikuli-X-1.0rc3 during 2012, when I decided to take over development and support and name it SikuliX | SikuliX automates anything you see on the screen of your desktop computer running Windows, Mac or some Linux/Unix. It uses image recognition powered by OpenCV to identify GUI components. This is handy in cases when there is no easy access to a GUI's internals or the source code of the application or web page you want to act on
feature list: operation 3501

SiliS-PTOXRA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0154
application sub category: topic 2840
application sub category: topic 3343
citation: ACS.CHEMRESTOX.9B00011
citation: pubmed:31066547
description: SiliS-PTOXRA (DRY-in Silico Screening & Prediction of Toxic Hazard and Risk Assessment) for the prediction of toxicological endpoints.
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: ptoxra
primary contact: César R. García-Jacas

SimBSI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3384
application sub category: topic 3855
citation: https://doi.org/10.1101/769679
description: An open-source Simulink library for developing closed-loop brain signal interfaces in animals and humans | Simulink Brain Signal Interface (SimBSI) | SimBSI is an open-source graphical environment for the rapid prototyping of animal and human brain-computer interfaces (BCIs). SimBSI is designed as a library on top of the graphical programming environment of Simulink with three goals in mind:
feature list: operation_0337
feature list: operation 3891
software help: Home

SimGEXPwMotifs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3173
application sub category: topic 3308
application sub category: topic 3315
citation: https://doi.org/10.1101/782615
description: Bayesian Linear Mixed Models for Motif Activity Analysis. Simulate gene expression data where gene expression is determined by a linear inlfuential factor, such as motifs.
feature list: operation 2426
feature list: operation 2495
feature list: operation 3659
license: MIT

SimPhospho
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: bty151
citation: pmcid:PMC6061695
citation: pubmed:29596608
description: Software tool enabling confident phosphosite assignment.
feature list: operation 3501
feature list: operation 3627
feature list: operation 3801
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: download
primary contact: Garry L Corthals
primary contact: Veronika Suni

SimRVSequences
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic 3053
application sub category: topic 3168
citation: btz881
citation: pmcid:PMC7141864
citation: pubmed:31764964
description: an R package to simulate genetic sequence data for pedigrees. Simulate Genetic Sequence Data for Pedigrees. Methods to simulate genetic sequence data for pedigrees, with functionality to simulate genetic heterogeneity among pedigrees. Christina Nieuwoudt, Angela Brooks-Wilson, and Jinko Graham (2019) <doi:10.1101/534552>
feature list: operation 3196
feature list: operation 3562
license: GPL-2.0

SimSpliceEvol
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0621
application sub category: topic_0623
application sub category: topic 3320
application sub category: topic 3512
citation: S12859-019-3207-5
citation: pmcid:PMC6916212
citation: pubmed:31842741
description: alternative splicing-aware simulation of biological sequence evolution. To add a sequence you need to click the "Add sequence" button is the top left corner of the main application screen. Sequences must be in the arc-annotated format: first line starts with > and following is the sequence header. Next line is the RNA Sequence and then the secondary structure inforamtion. You can add multitude sequences at the same time. The sequences will be added to the list in the side menu. To delete sequences, you can click on those you want deleted and click the "Delete selected" button to remove them. If you want to clear the whole list, the button "Delete all" will do it. The buttons "Select All" and "Unselect All" are used to make this easier when working with multiple sequences
feature list: operation_0232
feature list: operation_0491
feature list: operation 2499

SimVascular
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3335
application sub category: topic 3384
application sub category: topic 3474
citation: s11517-019-02029-3
citation: pmcid:PMC7250144
citation: pubmed:31446517
description: > MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'vessel pathlines', 'vessel', 'FCNN', 'vessel pathline' | Accelerating cardiovascular model building with convolutional neural networks | The only fully opensource software package providing a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis | Blood velocity distribution in CABG simulation | Blood velocity in coronary aneurism | SimVascular components svModel, svMesh, svPre, and svPost are provided under the full BSD license subject to the terms below: | Copyright © 1998-2007 Stanford University, Charles Taylor, Nathan Wilson, Ken Wang. See SimVascular Acknowledgements file for additional contributors to the source code

SimkaMin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3168
application sub category: topic 3174
application sub category: topic 3512
citation: BTZ685
citation: pubmed:31504187
description: fast and resource frugal de novo comparative metagenomics | Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets | This github directory stores Simka and SimkaMin software. This readme focuses on Simka features. All information about SimkaMin is located in the simkaMin directory
feature list: operation_0476
feature list: operation 3472
feature list: operation 3644
license: AGPL-3.0

SimpactCyan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 3305
application sub category: topic 3324
citation: S41598-019-55689-4
citation: pmcid:PMC6917719
citation: pubmed:31848434
description: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces.
feature list: operation 3562

SimpleDSFviewer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0130
citation: pro.3703
citation: pmcid:PMC6933846
citation: pubmed:31394001
description: A tool to analyze and view differential scanning fluorimetry data for characterizing protein thermal stability and interactions | Differential scanning fluorimetry (DSF) is a widely used thermal shift assay for measuring protein stability and protein-ligand interactions that are simple, cheap, and amenable to high throughput. However, data analysis remains a challenge, requiring improved methods. Here, the program SimpleDSFviewer, a user-friendly interface, is described to help the researchers who apply DSF technique in their studies. SimpleDSFviewer integrates melting curve (MC) normalization, smoothing, and melting temperature (Tm) analysis and directly previews analyzed data, providing an efficient analysis tool for DSF. SimpleDSFviewer is developed in Matlab, and it is freely available for all users to use in Matlab workspace or with Matlab Runtime. It is easy to use and an efficient tool for researchers to preview and analyze their data in a very short time

Simple ClinVar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic_0634
citation: GKZ411
citation: pmcid:PMC6602488
citation: pubmed:31114901
description: Interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database.
feature list: operation 3197
feature list: operation 3436
feature list: operation 3461
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: simple-clinvar.broadinstitute.org
software help: README.md
primary contact: Dennis Lal
primary contact: Eduardo Pérez-Palma
primary contact: Marie Gramm

SingleCellNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3170
citation: J.CELS.2019.06.004
citation: pmcid:PMC6715530
citation: pubmed:31377170
description: > HOMEPAGE MISSING! | A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species | Single-cell RNA-seq has emerged as a powerful tool in diverse applications, from determining the cell-type composition of tissues to uncovering regulators of developmental programs. A near-universal step in the analysis of single-cell RNA-seq data is to hypothesize the identity of each cell. Often, this is achieved by searching for combinations of genes that have previously been implicated as being cell-type specific, an approach that is not quantitative and does not explicitly take advantage of other single-cell RNA-seq studies. Here, we describe our tool, SingleCellNet, which addresses these issues and enables the classification of query single-cell RNA-seq data in comparison to reference single-cell RNA-seq data. SingleCellNet compares favorably to other methods in sensitivity and specificity, and it is able to classify across platforms and species
feature list: operation 3800

SingleCellSignalR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/2019.12.11.872895
description: Inference of intercellular networks from single-cell transcriptomics.
feature list: operation 3083
feature list: operation 3659

SinoPedia
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic 3474
citation: JOURNAL.PONE.0219992
citation: pmcid:PMC6677298
citation: pubmed:31374080
description: Linked Data Services platform for decentralized knowledge base | LodView is a powerful RDF viewer, IRI dereferencer and opensource SPARQL navigator | It is a long established fact that a reader will be distracted by the readable content of a page when looking at its layout. The point of using Lorem Ipsum is that it has a more-or-less normal distribution of letters, as opposed to using 'Content here, content here', making it look like readable English | Lorem Ipsum is simply dummy text of the printing and typesetting industry
feature list: operation 2422
feature list: operation 3559
feature list: operation 3760

SkinPhaser
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3303
application sub category: topic 3360
application sub category: topic 3518
citation: https://doi.org/10.1101/820811
description: A single-sample circadian biomarker that performs across populations and platforms. SkinPhaser is a Shiny app of predicing the circadian phase using expression values of 12 biomarker genes from human epidermis samples
feature list: operation_0269
feature list: operation 2495
feature list: operation 3454

SleepEEGNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic 3474
citation: JOURNAL.PONE.0216456
citation: pmcid:PMC6504038
citation: pubmed:31063501
description: Automated sleep stage scoring with sequence to sequence deep learning approach.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0002-3806-8487

SliceIt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic 3512
application sub category: topic 3534
citation: J.YMETH.2019.09.004
citation: pubmed:31494246
description: A genome-wide resource and visualization tool to design CRISPR/Cas9 screens for editing protein-RNA interaction sites in the human genome | Free Bootstrap 4 Pingendo Aquamarine template for unique events
feature list: operation 3096
feature list: operation 3901
feature list: operation 3902

Smart-3SEQ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: gr.234807.118
citation: pmcid:PMC6836736
citation: pubmed:31519740
description: > MEDIUM CONFIDENCE! | Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ | scripts used in the Smart-3SEQ paper
feature list: operation_0308
feature list: operation 2495
feature list: operation 3233

Smart Cancer Predictive System
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic 3360
application sub category: topic 3421
application sub category: topic 3512
application sub category: topic 3577
citation: S12935-019-1002-Z
citation: pmcid:PMC6854692
citation: pubmed:31754347
description: Two predictive precision medicine tools for hepatocellular carcinoma.
feature list: operation_0531
feature list: operation 3503
feature list: operation 3659

SmoothWin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3298
application sub category: topic 3337
citation: btz744
citation: pmcid:PMC7115897
citation: pubmed:31591642
description: Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data. Soft Windowing on Linear Regression. The main function in the package utilizes a windowing function in the form of an exponential weighting function to linear models. The bandwidth and sharpness of the window are controlled by two parameters. Then, a series of tests are used to identify the right parameters of the window (see Hamed Haselimashhadi et al (2019) <https://www.biorxiv.org/content/10.1101/656678v1>)
feature list: operation 2428
feature list: operation 3435
feature list: operation 3659
license: LGPL-2.0

Smudgeplots
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic 3315
citation: https://doi.org/10.1101/747568
description: Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568
feature list: operation 3192
feature list: operation 3196
feature list: operation 3472
license: Apache-2.0

Snorkel DryBell
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0605
application sub category: topic_0621
application sub category: topic 3474
citation: https://doi.org/10.1145/3299869.3314036
citation: pmcid:PMC6879379
citation: pubmed:31777414
description: A Case Study in Deploying Weak Supervision at Industrial Scale. Programmatically Building and Managing Training Data. Build Training Sets Programmatically. Labeling and managing training datasets by hand is one of the biggest bottlenecks in machine learning. In Snorkel, write heuristic functions to do this programmatically instead!

SnpHub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic 2885
application sub category: topic 3068
application sub category: topic 3168
citation: https://doi.org/10.1101/626705
description: Web-server framework to explore and visualize large genomic variation data in lab and its applications to wheat and its progenitors.
feature list: operation_0487
feature list: operation 3196
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: snphub tutorial
primary contact: Weilong Guo

SoS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0769
application sub category: topic 3855
citation: journal.pcbi.1006843
citation: pmcid:PMC6411228
citation: pubmed:30811390
description: Script of Scripts (SoS) is a computational environment for the development and execution of scripts in multiple languages for daily computational research.
feature list: operation 1812
feature list: operation 3196
feature list: operation 3431
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: content
primary contact: B. Peng

Solr-Plant
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0780
application sub category: topic 3050
application sub category: topic 3810
citation: S12859-019-2874-6
citation: pmcid:PMC6530169
citation: pubmed:31117932
description: Identification and resolution of plant taxonomic names.
feature list: operation_0495
feature list: operation 2421
feature list: operation 2422
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0003-2054-7356

SonicParanoid
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0084
application sub category: topic_0091
application sub category: topic_0797
author: https://orcid.org/0000-0002-1066-8659
citation: bty631
citation: pmcid:PMC6298048
citation: pubmed:30032301
description: SonicParanoid is a stand-alone software tool for the identification of orthologous relationships among multiple species.
feature list: operation_0292
feature list: operation_0324
feature list: operation 2423
feature list: operation 3209
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: usage
software version: 1.0.9
primary contact: https://orcid.org/0000-0002-1066-8659

SourceSet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3295
application sub category: topic 3518
citation: JOURNAL.PCBI.1007357
citation: pmcid:PMC6834292
citation: pubmed:31652275
description: A graphical model approach to identify primary genes in perturbed biological pathways. Topological gene-set analysis has emerged as a powerful means for omic data interpretation. Although numerous methods for identifying dysregulated genes have been proposed, few of them aim to distinguish genes that are the real source of perturbation from those that merely respond to the signal dysregulation. Here, we propose a new method, called SourceSet, able to distinguish between the primary and the secondary dysregulation within a Gaussian graphical model context. The proposed method compares gene expression profiles in the control and in the perturbed condition and detects the differences in both the mean and the covariance parameters with a series of likelihood ratio tests.
feature list: operation_0337
feature list: operation 2436
feature list: operation 3562
software help: index.html

SouthGreen platform
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0622
application sub category: topic_0780
application sub category: topic 3071
application sub category: topic 3810
citation: j.cpb.2016.12.002
description: The South Green platform is a local network of scientists gathering Bioinformatics skills based on the Agropolis campus that hosts research institutes such as CIRAD, IRD, INRA, SupAgro, Alliance of Bioversity international and CIAT. Based on this strong local community in the field of agriculture, food, biodiversity and environment, this network of national and international scope, develops bioinformatics applications and resources dedicated to genetics and genomics of tropical and Mediterranean plants. South Green relies on the computer technical platforms of its partner institutes.
software help: southgreen.fr
software help: trainings
software help: governance

South Green Genome Hubs
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
  encoding format: format 1929
output: Sequence
  type: FormalParameter
  additional type: data 2044
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic_0797
application sub category: topic 3308
application sub category: topic 3810
author: https://orcid.org/0000-0003-1849-1269
citation: j.xplc.2022.100330
citation: bat035
citation: uhac221
citation: gku1108
citation: pmcid:PMC3662865
citation: pmcid:PMC4383925
citation: pmcid:PMC9482989
citation: pmcid:PMC9720444
citation: pubmed:23707967
citation: pubmed:25392413
citation: pubmed:35617961
citation: pubmed:36479579
description: The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cacao, Coffee, Grass, Rice, Vanilla, Citrus and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).
feature list: operation_0338
feature list: operation 2403
feature list: operation 3208
is accessible for free: true
license: GPL-2.0
provider: https://orcid.org/0000-0003-1849-1269
software help: term-service
primary contact: https://orcid.org/0000-0003-1849-1269
primary contact: Mathieu Rouard

SoyCSN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3170
application sub category: topic 3308
citation: PLD3.167
citation: pmcid:PMC6747016
citation: pubmed:31549018
description: Soybean context-specific network analysis and prediction based on tissue-specific transcriptome data | SoyCSN (Soybean Context Specific Network) - | SoyCSN (Soybean Context Specific Network) | SoyCSN computes and visualizes any of the 14 soybean context specific networks both at the expression and interactome level. Users can compare the gene-gene relationship differences at different confidence levels across all the soybean tissues
feature list: operation 3439
feature list: operation 3463
feature list: operation 3766

SoyMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: A Soybean mine instance with genomic data from the Legume Information Systems (LIS) multi-species chado database and genetic data pulled from Soybase
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 0.10

SpCLUST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
citation: j.compbiomed.2019.103439
citation: pubmed:31550555
description: > HOMEPAGE MISSING! | Towards a fast and reliable clustering for potentially divergent biological sequences | This paper presents SpCLUST, a new C++ package that takes a list of sequences as input, aligns them with MUSCLE, computes their similarity matrix in parallel and then performs the clustering. SpCLUST extends a previously released software by integrating additional scoring matrices which enables it to cover the clustering of amino-acid sequences. The similarity matrix is now computed in parallel according to the master slave distributed architecture, using MPI. Performance analysis, realized on two real datasets of 100 nucleotide sequences and 1049 amino-acids ones, show that the resulting library substantially outperforms the original Python package. The proposed package was also intensively evaluated on simulated and real genomic and protein data sets. The clustering results were compared to the most known traditional tools, such as UCLUST, CD-HIT and DNACLUST

SpaCell
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3308
application sub category: topic 3382
application sub category: topic 3474
citation: https://doi.org/10.1101/837211
description: integrating tissue morphology and spatial gene expression to predict disease cells. SpaCell has been developed for analysing spatial transcriptomics (ST) data, which include imaging data of tissue sections and RNA expression data across the tissue sections. The ST data add a novel spatial dimension to the traditional gene expression data from dissociated cells. SpaCell is desinged to integrates the two histopathological imaging and sequencing fields, with the ultimate aim to discover novel biology and to improve histopathological diagnosis in a quantitative and automated way
feature list: operation 2454
feature list: operation 2495
feature list: operation 3799
license: MIT

SpaRC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3837
citation: https://doi.org/10.1101/620666
description: Apache Spark based Read Clustering tool to cluster a large number of DNA/RNA sequences generated from next-generation sequence technologies, including Illumina and PacBio.
feature list: operation_0310
feature list: operation 3432
feature list: operation 3629
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Zhong Wang

Spaced Radiology
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0749
application sub category: topic 3384
application sub category: topic 3444
citation: S00247-019-04415-3
citation: pmcid:PMC6598954
citation: pubmed:31093725
description: Encouraging durable memory using spaced testing in pediatric radiology.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
primary contact: https://orcid.org/0000-0003-1953-4486

Spaniel
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/619197
description: Spaniel Spatial Transcriptomics Analysis.
feature list: operation_0337
feature list: operation 3192
feature list: operation 3258
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: Spaniel Documentation
primary contact: Rachel Queen

Spark
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 2830
application sub category: topic 3315
application sub category: topic 3379
application sub category: topic 3474
citation: peerj.preprints.3260v2
description: Apache Spark is a unified analytics engine for big data processing, with built-in modules for streaming, SQL, machine learning and graph processing. Melanoma expression analysis with Big Data technologies.
feature list: operation_0252
feature list: operation 2495
feature list: operation 3659

SparkGA2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0654
application sub category: topic_0769
application sub category: topic 3168
application sub category: topic 3316
citation: JOURNAL.PONE.0224784
citation: pmcid:PMC6894754
citation: pubmed:31805063
description: Production-quality memory-efficient Apache Spark based genome analysis framework. SparkGA2 is an Apache Spark based scalable implementation of the best practice DNA analysis pipeline by Broad Institute, which is an improvement over the similar SparkGA1 (https://github.com/HamidMushtaq/SparkGA1.git)
feature list: operation_0487
feature list: operation 2409
feature list: operation 3432
license: GPL-3.0

SpatialDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
citation: gkz934
citation: pmcid:PMC7145543
citation: pubmed:31713629
description: a database for spatially resolved transcriptomes. Welcome to SpatialDB! click thumbnails to quickly browse the spatial gene expression profiles. Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology
feature list: operation_0337
feature list: operation 2495
feature list: operation 3501

Spectral Jaccard Similarity
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
citation: https://doi.org/10.1101/800581
description: A new approach to estimating pairwise sequence alignments. SimpleFastaParser from Bio.SeqIO.FastaIO. To create filtered datasets run Bacterial_pipeline_part1.py and Bacterial_pipeline_part2.py
feature list: operation_0491
feature list: operation 3198
feature list: operation 3695

SpikeInterface
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
citation: https://doi.org/10.1101/796599
description: SpikeInterface is an unified framework for spike sorting. Python-based module for extracting from, converting between, and interfacing with many common file formats in extracellular recording.
feature list: operation 2422
feature list: operation 2428
feature list: operation 3802

SpineJ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3382
application sub category: topic 3406
citation: https://doi.org/10.1101/764548
description: A software tool for quantitative analysis of nanoscale spine morphology | Abstract Super-resolution microscopy provides diffraction-unlimited optical access to the intricate morphology of neurons in living brain tissue, resolving their finest structural details, which are critical for neuronal function. However, as existing image analysis software tools have been developed for diffraction-limited images, they are generally not well suited for quantifying nanoscale structures like dendritic spines. We present SpineJ, a semi-automatic ImageJ plugin that is specifically designed for this purpose. SpineJ comes with an intuitive and user-friendly graphical user interface, facilitating fast, accurate, and unbiased analysis of spine morphology
feature list: operation 3450
feature list: operation 3799

SpliceFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0114
application sub category: topic 3320
application sub category: topic 3474
citation: S12859-019-3306-3
citation: pmcid:PMC6933889
citation: pubmed:31881982
description: ab initio prediction of splice sites using convolutional neural network. This is the source code for SpliceFinder
feature list: operation_0232
feature list: operation_0433
feature list: operation 3439

SpliceLauncher
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3512
application sub category: topic 3577
citation: BTZ784
citation: pubmed:31617569
description: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data. RNAseq pipeline for alternative splicing junctions. SpliceLauncher is a pipeline tool to study the alternative splicing. It works in three steps:. SpliceLauncher comes with a ready to use config.cfg file. It contains the paths of software and files used by SpliceLauncher. The INSTALL mode of SpliceLauncher updates this config.cfg file. If you define the path to GFF (v3) file and path to the FASTA genome, the INSTALL mode will extract all necessary information from this GFF and indexing the STAR genome. This informations are stored in a BED file that contains the exon coordinates, in a sjdb file that contains the intron coordinates and a text file that contains the details of transcript structures. You need to define where these files will saving by the -O, --output argument
feature list: operation 2499
feature list: operation 3225
feature list: operation 3800
license: MIT

SpliceV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3512
citation: S12859-019-2865-7
citation: pmcid:PMC6507234
citation: pubmed:31068132
description: Analysis and publication quality printing of linear and circular RNA splicing, expression and regulation.
feature list: operation_0264
feature list: operation_0433
feature list: operation_0446
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Erik Flemington

SpliceVec-g
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3307
application sub category: topic 3474
citation: j.compbiolchem.2018.03.009
citation: pubmed:29580738
description: SpliceVec: Distributed feature representations for splice junction prediction
feature list: operation_0337
feature list: operation 2990
operating system: Linux

SpliceVisuL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0160
application sub category: topic_0621
application sub category: topic 3474
citation: J.COMPBIOMED.2019.103558
citation: pubmed:31783254
description: Using the Chou's 5-steps rule to predict splice junctions with interpretable bidirectional long short-term memory networks. SpliceVisuL: Visualization of Bidirectional Long Short-term Memory Networks for Splice Junction Prediction
feature list: operation 2990
feature list: operation 3083

Spliceogen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3320
application sub category: topic 3512
citation: btz263
citation: pubmed:30993321
description: Integrative, scalable tool for the discovery of splice-altering variants.
feature list: operation_0264
feature list: operation_0433
feature list: operation_0446
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Steve Monger

SpydrPick
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3174
citation: GKZ656
citation: pmcid:PMC6765119
citation: pubmed:31361894
description: > MEDIUM CONFIDENCE! | Genome-wide epistasis and co-selection study using mutual information | SpydrPick is a command line tool for performing 'direct coupling analysis' of aligned categorical datasets. It constructs a coupling graph based on thresholded node-pair Mutual Information (MI) scoring, followed by pruning of edges that represent indirect couplings using the ARACNE algorithm | Mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure | Home: https://github.com/santeripuranen/SpydrPick | License: GNU Affero General Public License
feature list: operation_0484
feature list: operation 3227
feature list: operation 3461

Squiggle
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3068
application sub category: topic 3293
application sub category: topic 3382
citation: bty807
citation: pubmed:30247632
description: Software tool that automatically generates interactive web-based two-dimensional graphical representations of raw DNA sequences.
feature list: operation_0337
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: latest

SssI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0654
application sub category: topic 3295
application sub category: topic 3674
citation: S12859-019-3011-2
citation: pmcid:PMC6700779
citation: pubmed:31426747
description: A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction | This is our model of MBD pulldown alignments generated from SssI-treated DNA proposed in the publication entitled "A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction". Please read through the instructions in the README before using the software. Test files are provided in the "source" folder. Links to the indexes of CpGs in hg18 and the corresponding yi Λ file, generated from that list using our experimental presets and summed on 10bp windows, are also given
feature list: operation_0417
feature list: operation_0430
feature list: operation 3186

Sstack
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
citation: btz010
citation: pmcid:PMC6736036
citation: pubmed:30649230
description: R Package for Stacking with Applications to Scenarios Involving Sequential Addition of Samples and Features.
feature list: operation 3557
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.1
primary contact: Kevin Matlock

StackCBPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0160
application sub category: topic 3474
citation: J.CARRES.2019.107857
citation: pubmed:31683069
description: A stacking based prediction of protein-carbohydrate binding sites from sequence.
feature list: operation 2575

StanEx1
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3304
citation: G3.119.400105
citation: pmcid:PMC6643891
citation: pubmed:31040111
description: Interscholastic Network To Generate LexA Enhancer Trap Lines in Drosophila.
feature list: operation 3216
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
primary contact: Lutfi Huq
primary contact: Seung K. Kim

Staphopia
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3277
application sub category: topic 3489
citation: PEERJ.PREPRINTS.26890V2
description: Staphopia is a database focusing on the genomes of the bacterial pathogen Staphylococcus aureus. Life-threatening Methicillin-resistant S. aureus (MRSA) infections strike across our society, both in the community and hospital settings. In recent years whole genome shotgun sequencing of clinical isolates has become common. As of August 2017 there were over 44,000 publicly available S. aureus sequencing projects in EBI's ENA database. Staphopia aims to provide rapid analysis of these whole-genome datasets as well as useful S. aureus specific results, such as genotype, antibiotic resistance and virulence gene profiles.
feature list: operation 3211
feature list: operation 3431
feature list: operation 3482
feature list: operation 3840
license: MIT

StatAlign
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0082
application sub category: topic 3293
citation: 978-1-4939-8736-8 10
citation: msu184
citation: pmcid:PMC4137710
citation: pubmed:24899668
citation: pubmed:30298398
description: Extendable software package for Bayesian analysis of protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable quantification of the uncertainty in these estimates.
feature list: operation_0323
feature list: operation_0503
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: user manual.html
software help: statalign
primary contact: Adam Novak
primary contact: Joe Herman

StereoMate
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic 3382
citation: https://doi.org/10.1101/648337
description: Stereological and Automated Analysis Platform for Assessing Histological Labelling in Cleared Tissue Specimens.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: David L. Bennett
primary contact: Steven J. West

StoatyDive
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0160
application sub category: topic_0166
application sub category: topic 3169
application sub category: topic 3179
application sub category: topic 3794
citation: https://doi.org/10.1101/799114
description: Evaluation and Classification of Peak Profiles for Sequencing Data. StoatyDive is a tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets. It can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data. StoatyDive is a tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets
feature list: operation 2495
feature list: operation 2575
feature list: operation 3215
feature list: operation 3222
feature list: operation 3629
license: GPL-3.0

StrainHub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3293
application sub category: topic 3305
application sub category: topic 3324
citation: btz646
citation: pmcid:PMC8215912
citation: pubmed:31418766
description: A phylogenetic tool to construct pathogen transmission networks | Welcome to the StrainHub Repo - Files and Data - StrainHub Online: | Strainhub is designed as a web-based software to generate disease transmission networks and associated metrics from a combination of a phylogenetic tree and associated metadata. The software maps the metadata onto the tree and performs a parsimony ancestry reconstruction step to create links between the associated metadata and enable the construction of the network. Users also have the option to skip the StrainHub ancestry reconstruction step by generating a maximum clade credibility tree (MCC) through BEAST phylogeography | Generate disease transmission networks and associated metrics from a combination of a phylogenetic tree and associated metadata
feature list: operation_0545
feature list: operation_0555
feature list: operation 3478
license: GPL-3.0

StressGenePred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 3308
application sub category: topic 3360
application sub category: topic 3474
application sub category: topic 3518
citation: S12864-019-6283-Z
citation: pmcid:PMC6923958
citation: pubmed:31856731
description: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis. Stress predicting framework with microarray data based on CMCL and logical correlation model. Stress Predictor based on Machine Learning. python learn.py dataset/dataset_learn_v2_005.limma.csv dataset/dataset_learn_v2_005.label.csv --reduce_updown --save output/model_v2 --save_csv output/model_v2 --epoch_count 1000 --batch_size 0. --reduce_updown Use this parameter if dataset is separated into up and down column
feature list: operation 2436
feature list: operation 2454
feature list: operation 3196
feature list: operation 3565

String-pulling
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0625
application sub category: topic 3300
application sub category: topic 3304
application sub category: topic 3334
citation: https://doi.org/10.1101/2019.12.18.881342
description: This is a tool for analysis of video data of mice engaged in string-pulling. It analyses Phenotyping motor behavior of mice for sensory, whole-body and bimanual skilled hand function.
feature list: operation 3435
feature list: operation 3799
feature list: operation 3891
license: GPL-3.0

Stripes
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 2885
citation: S12711-019-0487-1
citation: pmcid:PMC6694510
citation: pubmed:31412777
description: > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'Genotyping low-coverage whole-genome sequencing intercross pedigrees from outbred founders' | Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders | Whole-genome genotyping in experimental pedigrees from outbred founders utilizing low coverage individual based sequencing | Carlborg's Lab (Yanjun Zan, Thibaut Payen, Örjan Carlborg) - BMC - Uppsala University | Experimental intercrosses of divergent lines are useful to map loci (quantitative trait loci; QTL) contributing to phenotypic variation using the recombinant founder mosaic genotypes in the F2 generation | git clone https://github.com/CarlborgGenomics/Stripes
feature list: operation_0282
feature list: operation 3196
feature list: operation 3557
license: GPL-3.0

StructAlign
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0154
citation: S0006297915110073
citation: pubmed:26615437
description: Program for alignment of structures of DNA-protein complexes.
feature list: operation_0295
feature list: operation_0303
feature list: operation_0492
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

StructureProfiler
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0082
application sub category: topic_0166
application sub category: topic_0196
citation: bty692
citation: pubmed:30124779
description: Tool for 3D protein structure profiling.
feature list: operation_0249
feature list: operation_0321
feature list: operation_0482
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Matthias Rarey

Struo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: https://doi.org/10.1101/774372
description: a pipeline for building custom databases for common metagenome profilers | Ley Lab MetaGenome Profiler DataBase generator | de la Cuesta-Zuluaga, Jacobo, Ruth E. Ley, and Nicholas D. Youngblut. 2019. “Struo: A Pipeline for Building Custom Databases for Common Metagenome Profilers.” bioRxiv. https://doi.org/10.1101/774372
feature list: operation_0310
feature list: operation 2495
feature list: operation 3460

StudyPortal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3063
application sub category: topic 3379
citation: S10916-019-1493-0
citation: pmcid:PMC6904404
citation: pubmed:31823031
description: StudyPortal combines the free sources ClinicalTrials.gov, PubMed, OpenStreetMap and Geonames.org to provide you an integrated search for visualization of suitable clinical studies and scientific articles that match your search criteria.
feature list: operation_0337
feature list: operation 2421
feature list: operation 2422

SuAVE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0153
application sub category: topic 3314
application sub category: topic 3448
citation: ACS.JCIM.9B00569
citation: pubmed:31508962
description: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces | SuAVE: Surface Assessment Via grid Evaluation
feature list: operation_0387
feature list: operation 1816

SuCOS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2258
application sub category: topic 2275
application sub category: topic 3336
citation: CHEMRXIV.8100203
description: RDKit-based overlap measure that combines volumetric shape and pharmacophoric features to give a combined overlap score similar to OpenEye's Tversky Combo and Malhotra and Karanicolas' COS measure.
feature list: operation_0337
feature list: operation_0482
feature list: operation 3216
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md

SubMito-XGBoost
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0209
application sub category: topic_0621
application sub category: topic_0634
application sub category: topic 2229
application sub category: topic 3407
citation: BTZ734
citation: pubmed:31603468
description: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting. MOTIVATION:Mitochondria are an essential organelle in most eukaryotes. They not only play an important role in energy metabolism but also take part in many critical cytopathological processes. Abnormal mitochondria can trigger a series of human diseases, such as Parkinson's disease, multifactor disorder, and Type-II diabetes. Protein submitochondrial localization enables the understanding of protein function in studying disease pathogenesis and drug design. RESULTS:We proposed a new method, SubMito-XGBoost, for protein submitochondrial localization prediction
feature list: operation_0253
feature list: operation 2489
feature list: operation 3092

Subdyquency
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic 2640
citation: S12859-019-2847-9
citation: pmcid:PMC6518800
citation: pubmed:31088372
description: Random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph.
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: 0000-0002-9572-951X

SugarSketcher
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0152
application sub category: topic 3314
citation: molecules23123206
citation: pmcid:PMC6320881
citation: pubmed:30563078
description: Intuitive and fast interface module for online drawing of glycan structures in the popular Symbol Nomenclature for Glycans (SNFG) notation and exporting them to various commonly used formats encoding carbohydrate sequences or quality images.
feature list: operation_0417
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows

Sugarcane Genome Hub
type: SoftwareApplication
input: Database search results
  type: FormalParameter
  additional type: data 2080
input: Sequence
  type: FormalParameter
  additional type: data 2044
input: Keyword
  type: FormalParameter
  additional type: data_0968
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
output: Sequence
  type: FormalParameter
  additional type: data 2044
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0091
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic 3810
author: https://orcid.org/0000-0003-1849-1269
citation: s41467-018-05051-5
citation: pmcid:PMC6035169
citation: pubmed:29980662
description: The Sugarcane Genome Hub is an integrated web-based database providing centralized access to the sugarcane reference genome sequences and genomic resources.
feature list: operation_0361
is accessible for free: true
license: GPL-2.0
operating system: Linux
software help: terms-service
primary contact: https://orcid.org/0000-0001-8869-3689

SulfAtlas
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0160
application sub category: topic 3068
application sub category: topic 3174
application sub category: topic 3293
citation: gkac977
citation: pmcid:PMC9825549
citation: pubmed:36318251
description: SulfAtlas describes the family and sub-families of structurally-related sulfatases. Sub-families are created based on phylogenetic analyses and essentially correspond to different substrate specificities
feature list: operation 2421
feature list: operation 2422
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

SumHer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3517
citation: s41588-018-0279-5
citation: pmcid:PMC6485398
citation: pubmed:30510236
description: Software for estimating confounding bias, SNP heritability, enrichments of heritability and genetic correlations using summary statistics from genome-wide association studies.
feature list: operation 3196
feature list: operation 3501
feature list: operation 3659
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Doug Speed

Sumer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0121
application sub category: topic_0602
application sub category: topic 2640
citation: mcp.tir118.001263
citation: pmcid:PMC6692773
citation: pubmed:31142576
description: An R package for summarizing multiple enrichment analysis results.
feature list: operation 2497
feature list: operation 3501
feature list: operation 3891
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Zhiao Shi

SummaryAUC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3517
citation: btz176
citation: pmcid:PMC6931355
citation: pubmed:30911754
description: Tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics.
feature list: operation_0484
feature list: operation 3196
feature list: operation 3557
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Jianxin Shi
primary contact: Lei Song

Super-Resolution
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3384
application sub category: topic 3474
application sub category: topic 3794
citation: TIP.2019.2940533
citation: pubmed:31545722
description: Image Super-Resolution as a Defense Against Adversarial Attacks | super-resolution-adversarial-defense | We use wavelet denoising and image super resolution as pre-processing steps to defend images against adversarial attacks. If you find our work useful in your research or publication, please cite our work:
feature list: operation 3629

SuperCRF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3474
citation: FONC.2019.01045
citation: pmcid:PMC6798642
citation: pubmed:31681583
description: Incorporating Global and Local Context for Enhanced Deep Learning in Melanoma Histopathology. Super CRF toolbox for training an conditional random field in combination with super pixel annotations

SuperCryoEMPicker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0611
application sub category: topic 3384
application sub category: topic 3444
citation: GENES10090666
citation: pmcid:PMC6770523
citation: pubmed:31480377
description: A Super-Clustering Approach for Fully Automated Single Particle Picking in Cryo-EM | A Super Clustering Approach for Single Particle Picking in cryo-EM Images
feature list: operation 3432
feature list: operation 3458

SureTypeSC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Script
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3518
citation: BTZ412
citation: pubmed:31116387
description: Random Forest and Gaussian Mixture predictor of high confidence genotypes in single cell data.
feature list: operation_0308
feature list: operation_0484
feature list: operation 3196
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Ivan Vogel

SurfCut
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2229
application sub category: topic 3382
citation: S12915-019-0657-1
citation: pmcid:PMC6509810
citation: pubmed:31072374
description: Pipeline for high-throughput extraction of cell contours from 3D image stacks.
feature list: operation 3446
feature list: operation 3799
is accessible for free: true
license: CECILL-C
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: SurfCut UserGuide.pdf
primary contact: https://orcid.org/0000-0003-3643-3978

SweGen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3399
application sub category: topic 3421
citation: pmcid:PMC6143968
description: P01.152 Evaluation of Factor V Leiden variant as risk a factor for venous thromboembolism in glioblastoma patients | The Swedish Frequency resource for genomics (SweFreq) is a website developed to make genomic datasets more findable and accessible in order to promote collaboration, new research and increase public benefit. You can contact swefreq@scilifelab.se if you want to find out more about this resource and how it could benefit you and your research | {{ mainCtrl.msg.level }}! {{ mainCtrl.msg.msg }}
feature list: operation 3196
feature list: operation 3659

SwiftOrtho
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0114
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic 3293
citation: GIZ118
citation: pmcid:PMC6812468
citation: pubmed:31648300
description: A fast, memory-efficient, multiple genome orthology classifier. A high performance tool to identify orthologs and paralogs across genomes. SwiftOrtho is orthology analysis tool which identifies orthologs, paralogs and co-orthologs for genomes. It is a graph-based approach
feature list: operation_0327
feature list: operation_0544
feature list: operation 2421
feature list: operation 3432
license: GPL-3.0

Swish
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: GKZ622
citation: pmcid:PMC6765120
citation: pubmed:31372651
description: > LOW CONFIDENCE! | Nonparametric expression analysis using inferential replicate counts | R scripts used in the Swish paper
feature list: operation 2495
feature list: operation 3223
feature list: operation 3800

SyQADA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0091
application sub category: topic_0769
application sub category: topic 3676
citation: gepi.22178
citation: pubmed:30565316
description: System for Quality-Assured Data Analysis (SyQADA) - workflow management system that seeks to improve reproducibility in as simple a framework as feasible.
feature list: operation 3431
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: Manual-2.0-RC2
primary contact: Paul Scheet

SyRI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3175
citation: S13059-019-1911-0
citation: pmcid:PMC6913012
citation: pubmed:31842948
description: SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.
feature list: operation_0310
feature list: operation_0487
feature list: operation 3196
feature list: operation 3198
feature list: operation 3227

SymPy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3569
citation: PEERJ.PREPRINTS.2083V2
citation: PEERJ.PREPRINTS.2083V3
description: Symbolic computing in Python. SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become the standard symbolic library for the scientific Python ecosystem. This paper presents the architecture of SymPy, a description of its features, and a discussion of select domain specific submodules. The supplementary materials provide additional examples and further outline details of the architecture and features of SymPy. SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become the standard symbolic library for the scientific Python ecosystem.

SynBioHub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 3398
application sub category: topic 3895
citation: YSZ016
citation: pmcid:PMC6690502
citation: pubmed:31423466
description: evaluation of free management platforms for synthetic biology designs | Web application enabling users and software to browse, upload, and share synthetic biology designs | Dumps all sequences from SynBioHub instances as FASTA | A parts repository for synthetic biology | SynBioHub is a design repository for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them. SynBioHub also facilitates searching for information about existing useful parts and designs by combining data from a variety of sources
feature list: operation 2422
feature list: operation 3431

SynQuant
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3304
application sub category: topic 3382
application sub category: topic 3474
citation: btz760
citation: pmcid:PMC8215930
citation: pubmed:31596456
description: An Automatic Tool to Quantify Synapses from Microscopy Images. A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images. SynQuant is a Fiji plugin that automatically quantify synapses from fluorescence microscopy images. Try SynQuant Now!. SynQuant performs better than peer unsupervised methods [5-8] for all the three data sets we tested (3D in-vivo [2], array tomography [3], neuron-astrocyte coculture [4])
feature list: operation 3435
feature list: operation 3450
feature list: operation 3799
license: GPL-3.0

SynTViewTools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
description: Specific tools for pre-processing datas in order to use them in SynTView.

SyntDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: gkz941
citation: pmcid:PMC7145678
citation: pubmed:31728519
description: SyntDB: defining orthologues of human long noncoding RNAs across primates. SyntDB - the database of human long non-coding RNAs conserved across primates. Comprehensive collection of long noncoding RNAs (lncRNAs) and their evolutionary relationships in twelve primate species, including human
feature list: operation 2422

Synteny Browser
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0091
application sub category: topic_0102
application sub category: topic_0749
application sub category: topic_0797
citation: S00335-019-09821-4
citation: pmcid:PMC6892358
citation: pubmed:31776723
description: The JAX Synteny Browser for mouse-human comparative genomics. An interactive web-based conserved synteny browser application. The Jackson Laboratory Synteny Browser. An interactive web-based conserved synteny browser application, The Jackson Laboratory (JAX) Synteny Browser. The browser allows researchers to highlight or selectively display genome features in the reference and/or the comparison genomes based on the biological attributes of the features. The current implementation for the browser supports the reference genomes of the laboratory mouse and human. Show true orientation of comparison genome relative to reference Always show gene symbols Show anchors. Reference species (outer ring) Mus musculus Homo sapiens
feature list: operation 3194
feature list: operation 3208
feature list: operation 3209
license: CC-BY-4.0

T-Gene
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0204
application sub category: topic_0621
application sub category: topic_0749
application sub category: topic 3295
application sub category: topic 3512
citation: https://doi.org/10.1101/803221
description: Improved target gene prediction. Abstract Motivation Identifying the genes regulated by a given transcription factor (its “target genes”) is a key step in developing a comprehensive understanding of gene regulation. Previously we developed a method for predicting the target genes of a transcription factor (TF) based solely on the correlation between a histone modification at the TF’s binding site and the expression of the gene across a set of tissues. That approach is limited to organisms for which extensive histone and expression data is available, and does not explicitly incorporate the genomic distance between the TF and the gene. Results We present the T-Gene algorithm, which overcomes these limitations. T-Gene can be used to predict which genes are most likely to be regulated by a TF, and which of the TF’s binding sites are most likely involved in regulating particular genes.
feature list: operation_0445
feature list: operation 2575
feature list: operation 3463

T-Library
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0218
application sub category: topic 3379
application sub category: topic 3473
citation: PEERJ.PREPRINTS.27685V2
citation: PEERJ.PREPRINTS.27685V3
description: Automated data extraction software for medical summary using text mining (T-Library). Library project of Physician’s empirical knowledge. Automatic extraction of medical information from medical record. Yamada T, Kondo Y, Momosaki R. 2019. Automated data extraction software for medical summary using text mining (T-Library) PeerJ Preprints 7:e27685v1 https://doi.org/10.7287/peerj.preprints.27685v1
feature list: operation_0306

T-MTSCCA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2885
application sub category: topic 3384
application sub category: topic 3444
citation: BTZ320
citation: pmcid:PMC6613037
citation: pubmed:31510645
description: Identifying progressive imaging genetic patterns via multi-task sparse canonical correlation analysis | temporal multi-task sparse canonical correlation analysis | T-MTSCCA: temporal multi-task SCCA model for longitudinal brain imagign genetics
feature list: operation 3196
license: GPL-3.0

T-lex3
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 3168
citation: btz727
citation: pmcid:PMC7703783
citation: pubmed:31580402
description: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data. Release 3: Maria Bogaerts maria.bogaerts@ibe.upf-csic.es, Josefa Gonzalez josefa.gonzalez@ibe.upf-csic.es. T-lex is a computational pipeline that detects presence and/or absence of annotated individual transposable elements (TEs) using next-generation sequencing (NGS) data. Problems during installation? Try our DOCKER file.
feature list: operation 3196
feature list: operation 3198
license: GPL-3.0

T-psi-C
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 3047
application sub category: topic 3170
application sub category: topic 3489
citation: gkz922
citation: pmcid:PMC7145666
citation: pubmed:31624839
description: user friendly database of tRNA sequences and structures. Discover the best tRNA database available!. There is simplified list of what you can do:. Search by sequence, structure and other properties. See available and generated models
feature list: operation_0337
feature list: operation_0464
feature list: operation 2421
feature list: operation 2422

T1D
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3379
application sub category: topic 3390
application sub category: topic 3418
citation: https://doi.org/10.2196/13724
citation: pmcid:PMC6701161
citation: pubmed:31389338
description: > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'mDAD', 'T1DToolkit.org' | Designing Online and Mobile Diabetes Education for Fathers of Children With Type 1 Diabetes | T1D Toolkit – Manage Diabetes Better | Research QuestionBlog Post FeedbackTech Support | This field is for validation purposes and should be left unchanged

T1TAdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3170
application sub category: topic 3512
citation: rna.078802.121
citation: pmcid:PMC8594479
citation: pubmed:34531327
description: T1TAdb is a database of Type I Toxin-Antitoxin systems.
feature list: operation_0267
feature list: operation_0278
feature list: operation_0346
feature list: operation 2488
primary contact: Fabien Darfeuille
primary contact: Nicolas J. Tourasse

TACITuS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3518
citation: S12859-019-2912-4
citation: pmcid:PMC6873396
citation: pubmed:31757212
description: TACITuS is a portal, which deals with data pre-processing, selection and, eventually, integration of transcriptomic data coming from diverse sources, such as ArrayExpress.
feature list: operation 2422
feature list: operation 2495
feature list: operation 3435

TAD-Lactuca
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3295
application sub category: topic 3512
application sub category: topic 3673
citation: S12864-019-6303-Z
citation: pmcid:PMC6933632
citation: pubmed:31881832
description: A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information. TAD-Lactuca is a tool to predict Topologically Associating Domains(TAD) boundary using histone marks information. It was written in Python language, using Random Forests(RF) and Multilayer Perception(MLP)
feature list: operation_0303
feature list: operation_0438
feature list: operation 2404

TADA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 3293
application sub category: topic 3697
citation: BTZ394
citation: pmcid:PMC6612822
citation: pubmed:31510701
description: phylogenetic augmentation of microbiome samples enhances phenotype classification | TADA is a new data augmentation technique for classifying phenotypes based on the microbiome. Our algorithm, TADA, uses available data and a statistical generative model to create new samples augmenting existing ones, addressing issues of low-sample-size. In generating new samples, TADA takes into account phylogenetic relationships between microbial species. Adding these synthetic samples to the training set improves the accuracy of downstream classification, especially when the training data have an unbalanced representation of classes

TAGOOS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2885
application sub category: topic 3512
application sub category: topic 3517
citation: gkz320
citation: pmcid:PMC6698643
citation: pubmed:31045203
description: Genome-wide supervised learning of non-coding loci associated to complex phenotypes.
feature list: operation_0488
feature list: operation 3232
feature list: operation 3661
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: tagoos.readthedocs.io

TAMMiCol
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic 3382
application sub category: topic 3557
application sub category: topic 3697
citation: journal.pcbi.1006629
citation: pmcid:PMC6292648
citation: pubmed:30507938
description: Tool for analysis of the morphology of microbial colonies.
feature list: operation_0417
feature list: operation 3443
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Mac
operating system: Windows
software help: UserGuide.pdf
primary contact: H. Tronnolone

TAPAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3534
citation: bty110
citation: pmcid:PMC6454472
citation: pubmed:30052912
description: Tool for alternative polyadenylation site analysis.
feature list: operation 2575
feature list: operation 3798
feature list: operation 3800
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Tao Jiang
primary contact: Xinshu Xiao

TAR-VIR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3174
application sub category: topic 3837
citation: s12859-019-2878-2
citation: pmcid:PMC6549370
citation: pubmed:31164077
description: Pipeline for TARgeted VIRal strain reconstruction from metagenomic data.
feature list: operation_0310
feature list: operation_0487
feature list: operation 2495
is accessible for free: true
license: Unlicense
operating system: Linux
software help: Guidance for Installing PEHaplo and TAR-VIR.md
software help: README.md

TARA BLAST Service
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
output: Sequence search results
  type: FormalParameter
  additional type: data_0857
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0622
description: BLAST service for the entire “TARA OCEANS” collection, an international project to which many researchers of the institute cooperated. It includes assembled sequences of prokaryotic and eukaryotic fractions.
feature list: operation_0346
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

TASBE Flow Analytics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0769
application sub category: topic 3382
application sub category: topic 3895
citation: ACSSYNBIO.8B00533
citation: pubmed:31053031
description: Package for Calibrated Flow Cytometry Analysis.
feature list: operation 3501
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: TASBEFlowAnalytics-tutorial
primary contact: Jacob Beal

TAXyl
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0121
application sub category: topic_0821
application sub category: topic 3297
application sub category: topic 3474
citation: https://doi.org/10.1101/826040
description: An in-silico method for predicting the thermal activity for xylanases from GH10 and GH11 families. a multi-step method for the classification of xylanases from glycoside hydrolases families 10 and 11 based on their optimum temperature of activity. TAXyl: An in-silico method for predicting the optimum temperature of activity for xylanases from GH10 and GH11 families. Xylanases are involved in lignocellulosic biomass degradation and the enzyme optimum temperature is an essential factor to be considered for choosing an appropriate biocatalyst for specific usage
feature list: operation_0474
feature list: operation 1777
feature list: operation 3092
license: MIT

TB Portals
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
additional type: Database portal
additional type: Web application
application sub category: topic_0634
application sub category: topic 2885
application sub category: topic 3063
application sub category: topic 3324
application sub category: topic 3384
citation: J.MEEGID.2019.104137
citation: https://doi.org/10.1101/833954
citation: pubmed:31838261
description: Prediction of multiple drug resistant pulmonary tuberculosis against drug sensitive pulmonary tuberculosis by CT nodular consolidation sign. International partnership for clinical informatics. and advanced research in tuberculosis. Leveraging clinical, genomic, and imaging data.

TCGA-LGG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic 3360
application sub category: topic 3518
citation: PEERJ.7414
citation: pmcid:PMC6752186
citation: pubmed:31576231
description: Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma.
feature list: operation_0531
feature list: operation 3503
feature list: operation 3659

TCGenerators
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3293
citation: JOURNAL.PCBI.1007347
citation: pmcid:PMC6756559
citation: pubmed:31509525
description: > MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'tree-child', 'BTC' | Generation of Binary Tree-Child phylogenetic networks | Supplementary files for "Generation of Tree-Child phylogenetic networks" | If you have pipenv installed, the requirements can be installed by executing pipenv install. Notice however that graphviz must be installed previously (only needed to run the Jupyter notebook). Once installed, the jupyter notebooks can be run with pipenv run jupyter-notebook, and the scripts with pipenv run python script.py | The jupyter notebook can also be run without installing anything:
feature list: operation_0552
feature list: operation_0555
feature list: operation 3478

TCMSP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0140
application sub category: topic_0202
application sub category: topic_0749
application sub category: topic 3068
application sub category: topic 3407
citation: https://doi.org/10.1155/2019/2160175
citation: pmcid:PMC6874874
citation: pubmed:31781261
description: A Network Pharmacology Approach for Uncovering the Osteogenic Mechanisms of Psoralea corylifolia Linn.
feature list: operation 2436
feature list: operation 2489

TCRE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0218
application sub category: topic_0602
application sub category: topic_0749
citation: https://doi.org/10.1101/643767
description: T Cell Relation Extraction (TCRE) - Extracting T Cell Function and Differentiation Characteristics from the Biomedical Literature.
feature list: operation_0306
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Eric Czech

TCRex
type: SoftwareApplication
input: Protein sequence record
  type: FormalParameter
  additional type: data 2886
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3168
citation: https://doi.org/10.1101/373472
description: The TCRex web tool provides a user-friendly interface to predict the recognition of pathogenic & cancer epitopes by human T cell receptors (TCRs). It can predict TCR–epitope binding based on TCR beta chain information from full repertoire data files from standard files (Immunoseq, MiXCR, etc), and calculates appropriate statistics.
feature list: operation_0252
feature list: operation 2403
feature list: operation 2995
feature list: operation 3501
is accessible for free: true
software help: instructions
software version: v0.2.1

TCRpMHCmodels
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0077
application sub category: topic_0154
application sub category: topic_0804
application sub category: topic 2275
citation: S41598-019-50932-4
citation: pmcid:PMC6787230
citation: pubmed:31601838
description: Structural modelling of TCR-pMHC class I complexes. Structural modeling tool of TCR-pMHC class I complexes. TCRpMHCmodels predicts the three-dimensional structure of TCR-pMHC class I complexes using comparative modelling. Upon submission, this tool automatically selects the best templates and provides within minutes a complete three-dimensional model. The input must include all protein chains from the TCR-pMHC complex (the TCR alpha chain, the TCR beta chain, the peptide chain and the MHC chain), separated by a fasta header. The tool will automatically detect the chain types
feature list: operation_0321
feature list: operation_0477
feature list: operation 3899

TCSM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic 2640
citation: BTZ340
citation: pmcid:PMC6612886
citation: pubmed:31510643
description: > CORRECT NAME OF TOOL COULD ALSO BE 'IMPLEMENTATION:TCSM' | Modeling clinical and molecular covariates of mutational process activity in cancer | Tumor Covariate Signature Model (TCSM) | This repository contains the code for reproducing the results on real data from the paper Modeling Clinical and Molecular Covariates of Mutational Process Activity in Cancer, which implements the Tumor Covariate Signature Model (TCSM)
feature list: operation_0239
feature list: operation 3557
license: MIT

TCSRWRLD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 2640
citation: S12859-019-3216-4
citation: pmcid:PMC6889579
citation: pubmed:31795943
description: A novel target convergence set based random walk with restart for prediction of potential LncRNA-disease associations.

TCW
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/733311
description: analysis of single and comparative transcriptomes | Download TCW package: www.agcol.arizona.edu/software/tcw or from this site | Transcriptome Computational Workbench | AGCoL : TCW Home : Doc Index : singleTCW Guide : DE Guide : multiTCW Guide : Tour | Description: For single-transcriptome (singleTCW) - similarity search against annotation databases, GO annotation, ORF finding and differential analysis. For multi-transcriptome (multiTCW) - compute similar pairs, provide statistics for pairs, compute clusters, provide statistics for clusters. Both singleTCW and multiTCW provide graphical interfaces for extensive query and display of the results | TCW provides analysis and query for sequences (transcriptome, proteome), and comparison of species sequences. TCW uses Java, mySQL, optionally R, and various External packages. It has been tested on Linux and Mac
feature list: operation_0224
feature list: operation_0436
feature list: operation 3644
license: GPL-3.0

T-Coffee API (EBI)
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0080
citation: jmbi.2000.4042
citation: pubmed:10964570
description: Multiple sequence alignment program. The main characteristic is that it will allow you to combine results obtained with several alignment methods.
feature list: operation_0492
feature list: operation 2403
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: tcoffee rest
software version: 1

T-Coffee (EBI)
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0080
author: Cedric Notredame
citation: jmbi.2000.4042
citation: gkac240
citation: gkae241
citation: pmcid:PMC11223882
citation: pmcid:PMC9252731
citation: pubmed:10964570
citation: pubmed:35412617
citation: pubmed:38597606
description: Multiple sequence alignment that combines several alignment methods.
feature list: operation_0492
feature list: operation 2403
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
provider: CRG
provider: EMBL-EBI
software help: terms-of-use
software help: index.html
software help: help
software version: 1
primary contact: Job Dispatcher

T-Coffee (SIB)
type: SoftwareApplication
input: Sequence
  type: FormalParameter
  additional type: data 2044
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
additional type: Web application
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0622
citation: gkr245
citation: pmcid:PMC3125728
citation: pubmed:21558174
description: A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures. Includes M-Coffee, R-Coffee, Expresso, PSI-Coffee, iRMSD-APDB.
feature list: operation_0492
feature list: operation 2403
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: tcoffee
primary contact: http://orcid.org/0000-0003-1461-0988

TDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3384
application sub category: topic 3444
citation: NETN A 00091
citation: pmcid:PMC6663192
citation: pubmed:31410373
description: > LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'Betti', 'resting-state' | Exact topological inference of the resting-state brain networks in twins | Exact Topological Inference (ETI) for Brain Networks | The data/codes presented here is published in [4,5,6]. Using the data, we will show how to construct Betti plots from weighted brain graphs, where the weights are Pearson correlations. Then show how to perform the exact topological inference and obtain the p-value on the Betti plots. The Betti plots are the basic data visualization technique in persistent homology but statistical inference procedure has been lacking in the field [1,2,3]. New exact topological inference framework is developed for determining statistical significance of Betti plots | The codes have been tested with MacBook Pro with MATLAB 2016
feature list: operation 3216
feature list: operation 3562

TDNAscan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 3168
application sub category: topic 3519
citation: FGENE.2019.00685
citation: pmcid:PMC6690219
citation: pubmed:31428129
description: > HOMEPAGE MISSING! | A Software to Identify Complete and Truncated T-DNA Insertions | Transfer (T)-DNA insertions in mutants isolated from forward genetic screens are typically identified through thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR), inverse PCR, or plasmid rescue. Despite the popularity and success of these methods, they have limited capabilities, particularly in situations in which the T-DNA is truncated. Here, we present a next generation sequencing (NGS)-based platform to facilitate the identification of complete and truncated T-DNA insertions. Our method enables the detection of the corresponding T-DNA insertion orientation and zygosity as well as insertion annotation. This method, called TDNAscan, was developed to be an open source software
feature list: operation_0308
feature list: operation 3192
feature list: operation 3196

TDimpute
type: SoftwareApplication
input: Data
  type: FormalParameter
  additional type: data_0006
  encoding format: format 3752
output: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
application sub category: topic_0091
application sub category: topic 3170
application sub category: topic 3173
application sub category: topic 3474
citation: https://doi.org/10.1101/803692
description: TDimpute is a novel transfer learning-based neural network to impute missing gene expression data from DNA methylation data. In the tool, the pan-cancer dataset from TCGA was utilized for training a general model for all cancers, which was then fine-tuned on the target cancer dataset for imputation.
feature list: operation 3557
is accessible for free: true
operating system: Linux
software help: TDimpute
software version: 0.0.1

TE-Tracker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0622
application sub category: topic 3673
description: TE-Tracker is a program for detecting germline transposition events through whole-genome resequencing.

TECH-VER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 3068
application sub category: topic 3305
citation: S40273-019-00844-Y
citation: pmcid:PMC6860463
citation: pubmed:31705406
description: A Verification Checklist to Reduce Errors in Models and Improve Their Credibility. This is the model verification repository. An application example is uploaded on the repository. This example will be updated further and with other elaborated examples. The TECH-VER checklist consists of five domains: (1) input calculations; (2) event-state (patient flow) calculations; (3) result calculations; (4) uncertainty analysis calculations; and (5) other overall checks (e.g. validity or interface). In health economic literature, checklists or best practice recommendations on model validation credibility always declare verification of the programmed model as a fundamental step, such as ‘is the model implemented correctly and does the implementation accurately represent the conceptual model?’ However, to date, little operational guidance for the model verification process has been given
feature list: operation_0305
feature list: operation 2422
feature list: operation 3435

TEF
type: SoftwareApplication
input: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1476
output: Protein property
  type: FormalParameter
  additional type: data_0897
  encoding format: format 1957
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0736
citation: https://doi.org/10.1080/07391102.2018.1546230
citation: pubmed:30585105
description: Graph-based computational method for decomposing protein structures into closed loops.
feature list: operation_0246
is accessible for free: true
license: Freeware
software help: tef2.github.io
software version: 2.0
primary contact: https://orcid.org/0000-0002-0380-0092
primary contact: https://orcid.org/0000-0002-4250-0762
primary contact: https://orcid.org/0000-0002-7373-0181

TEGS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0128
application sub category: topic_0203
citation: TCBB.2019.2916038
citation: pubmed:31095490
description: Prediction of essential proteins by integrating network topology, subcellular localization information, gene expression profile and GO annotation data.
feature list: operation 2489
feature list: operation 2492
feature list: operation 2495
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Wei Zhang

TEMPO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3399
citation: https://doi.org/10.1101/651018
description: TEMPO (TEmporal Modeling of Pathway Outliers) - method for modeling and detecting gene sets with disruption of some temporal pattern of expression.
feature list: operation 2436
feature list: operation 3431
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: tempoR.pdf
primary contact: Christopher Pietras

TEffectR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3295
citation: PEERJ.8192
citation: pmcid:PMC6899341
citation: pubmed:31824778
description: TEffectR is an R package for studying the potential effects of transposable elements on gene expression with linear regression model.
feature list: operation 2495
feature list: operation 3659
feature list: operation 3799
license: GPL-3.0

TEs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0199
citation: TPJ.14489
citation: pubmed:31381222
description: > CORRECT NAME OF TOOL COULD ALSO BE 'maizeTE_variation' | Transposable elements contribute to dynamic genome content in maize | Structural transposable element (TE) annotation of multiple maize genomes | TEs along a region of the genome: | We reconstruct the history of TEs nesting into each other. For example, the blue TE on the left inserted first, and then was disrupted by the insertion of green and yellow TEs
feature list: operation_0487
feature list: operation 3196
feature list: operation 3216

TEsorter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0736
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3293
citation: https://doi.org/10.1101/800177
description: lineage-level classification of transposable elements using conserved protein domains. Note: do not move or hard link TEsorter.py alone to anywhere else, as it rely on database/ and bin/. You can add the directory to PATH or soft link TEsorter.py to PATH
feature list: operation 3478

TFBSshape
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3295
application sub category: topic 3674
citation: gkz970
citation: pmcid:PMC7145579
citation: pubmed:31665425
description: an expanded motif database for DNA shape features of transcription factor binding sites. Responsive Bootstrap 4 Admin & Dashboard Template. TFBSshape provides DNA shape features for transcription factor binding sites (TFBSs). These structural features refine the description of TF binding specificities and provide mechanistic insights into protein–DNA recognition. The DNA shape features were predicted using our recently published high-throughput method (Zhou et al. NAR 2013) and visualized in the form of heat maps. Users can download these DNA shape feature data and perform further analysis, for example, to identify which DNA shape feature(s) at which position(s) in the target DNA contribute to the DNA binding specificity of a TF. Users can also compare DNA shape profiles, both qualitatively and quantitatively, between two TF datasets from the database, or between a set of uploaded sequences and a TF from the database
feature list: operation_0337
feature list: operation_0445
feature list: operation 3092
feature list: operation 3891
feature list: operation 3894

TFmiR2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3512
citation: BTZ871
citation: pubmed:31746988
description: Constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks. It seems like you are using Internet Explorer, which is not supported yet. Please switch to Chrome , Firefox , or Safari
feature list: operation_0463
feature list: operation 3083
feature list: operation 3792

TFregulomeR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3173
application sub category: topic 3512
application sub category: topic 3674
citation: gkz1088
citation: pmcid:PMC6954419
citation: pubmed:31754708
description: TFregulomeR comprises of a comprehensive compendium of transcription factor binding sites (TFBSs) derived from the MethMotif and GTRD, as well as the ready-to-use functionality in R language facilitating data access, integration and analysis. The binding motifs predicted in-silico from MethMotif and GTRD describe cell specific transcription factor (TF) binding propensities, while the DNA methylation profiles from MethMotif portray a second epigenetic dimension in TF binding events. The whole toolbox allows a better understanding of the TF binding propensities in a cell-specific manner.
feature list: operation_0268
feature list: operation_0445
feature list: operation 3222
feature list: operation 3900
feature list: operation 3903

TGS-GapCloser
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0749
application sub category: topic 3168
citation: https://doi.org/10.1101/831248
description: TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.
feature list: operation_0525
feature list: operation 3183
feature list: operation 3198
feature list: operation 3216

TGS-Lite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 3474
application sub category: topic 3518
citation: https://doi.org/10.1101/755249
description: Rapid Reconstruction of Time-varying Gene Regulatory Networks with Limited Main Memory | Abstract Reconstruction of time-varying gene regulatory networks underlying a time-series gene expression data is a fundamental challenge in the computational systems biology. The challenge increases multi-fold if the target networks need to be constructed for hundreds to thousands of genes. There have been constant efforts to design an algorithm that can perform the reconstruction task correctly as well as can scale efficiently (with respect to both time and memory) to such a large number of genes. However, the existing algorithms either do not offer time-efficiency, or they offer it at other costs memory-inefficiency or imposition of a constraint, known as the ‘smoothly time-varying assumption’
feature list: operation_0277
feature list: operation 1781
feature list: operation 3439

THBP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic 3067
citation: S12859-019-3005-0
citation: pmcid:PMC6697955
citation: pubmed:31419946
description: Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries | *: Background Consisting of dictated free-text documents such as discharge summaries, medical narratives are widely used in medical natural language processing. Relationships between anatomical entities and human body parts are crucial for building medical text mining applications. To achieve this, we establish a mapping system consisting of a Wikipedia-based scoring algorithm and a named entity normalization method (NEN). The mapping system makes full use of information available on Wikipedia, which is a comprehensive Internet medical knowledge base
feature list: operation 2429
feature list: operation 3280
feature list: operation 3432

THESIAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3055
citation: sj.ejhg.5201238
citation: btm058
citation: https://doi.org/10.1093/hmg/11.17.2015
citation: pubmed:12165563
citation: pubmed:15241485
citation: pubmed:17308338
description: Testing Haplotype Effects In Association Studies
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 3.1

TILLinG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic_0605
application sub category: topic_0625
application sub category: topic 3676
citation: FPLS.2019.01244
citation: pmcid:PMC6795695
citation: pubmed:31649706
description: Bioinformatics pipeline for the analysis of TILLinG mutants in conjunction with the new optimised reference sequence for tetraploid wheat. This tool consists of TILLING populations developed in tetraploid durum wheat cv 'Kronos' and hexaploid bread wheat cv 'Cadenza' as part of a joint project between the University of California Davis, Rothamsted Research, The Earlham Institute, and John Innes Centre.
feature list: operation 3196
feature list: operation 3198
feature list: operation 3227
feature list: operation 3229
feature list: operation 3431

TITAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0176
application sub category: topic_0821
application sub category: topic 3314
citation: JCC.26072
citation: pubmed:31568581
description: A Code for Modeling and Generating Electric Fields-Features and Applications to Enzymatic Reactivity. TITAN (elecTric fIeld generaTion And maNipulation) is being developed by:
feature list: operation_0386
feature list: operation 2476

TITINdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0593
application sub category: topic_0634
citation: btx424
citation: pmcid:PMC5860166
citation: pubmed:29077808
description: Computational tool to assess titin’s role as a disease gene.
feature list: operation 3225
feature list: operation 3226
feature list: operation 3227
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation
software help: tutorials
primary contact: Franca Fraternali

TKR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3315
application sub category: topic 3379
application sub category: topic 3421
citation: CTS.2019.380
citation: pmcid:PMC6676499
citation: pubmed:31404154
description: The use of patient-specific equipoise to support shared decision-making for clinical care and enrollment into clinical trials | Total Knee Replacement (TKR) Decision Support | TMC Total Knee Replacement (TKR) Math Equipoise | Welcome to the Knee Arthritis Treatment Tool
feature list: operation 3557
feature list: operation 3659

TM-IMC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic 3300
citation: ACSOMEGA.8B02454
citation: pmcid:PMC6649004
citation: pubmed:31459527
description: Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion | TM-IMC: Text Mining and Induce Matrix Completion for GPCR function prediction | TM-IMC is an algorithm for automated annotation of Gene Ontology (GO) term for G protein-coupled receptors (GPCRs) using features derived from text mining and induced matrix completion of GPCR-GO associatation matrix
feature list: operation_0267
feature list: operation_0306
feature list: operation_0480

TM3 seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0610
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: g3.119.400821
citation: pmcid:PMC6945013
citation: pubmed:31676507
description: A Tagmentation-Mediated 3' Sequencing Approach for Improving Scalability of RNAseq Experiments.
feature list: operation 3196
feature list: operation 3200
feature list: operation 3435
feature list: operation 3800

TMAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3174
application sub category: topic 3293
application sub category: topic 3697
citation: BTZ686
citation: pubmed:31504188
description: Phylogenetic Tree-based Microbiome Association Test | Ecological patterns of the human microbiota exhibit high inter-subject variation, with few operational taxonomic units (OTUs) shared across individuals
feature list: operation_0325
feature list: operation_0499
feature list: operation 3478

TMB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3125
application sub category: topic 3176
application sub category: topic 3368
citation: ACS.JCIM.9B00252
citation: pubmed:31490686
description: > LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'iBIOMES', 'Lite', 'iBIOMES Lite', 'nucleosome' | TMB Library of Nucleosome Simulations | Nucleosomes are the fundamental building blocks of chromatin, the biomaterial that houses the genome in all higher organisms. A nucleosome consists of 145-147 base pairs of DNA wrapped 1.7 times around eight histones. Given a four-letter code (A, C, G, T), there are approximately 4147 or 1088 oligonucleotides that can form a nucleosome. Comparative, rather than comprehensive, studies are required. Here we introduce the TMB Library of nucleosome simulations and present a meta-analysis of over 20 μs of all atom molecular dynamics simulations representing 518 different realizations of the nucleosome. The TMB Library serves as a reference for future comparative, on-demand simulations of nucleosomes and a demonstration of iBIOMES Lite as a tool for managing a laboratory's simulation library
feature list: operation_0244
feature list: operation_0478
feature list: operation 2476

TMPfold
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0130
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic_0736
application sub category: topic_0820
citation: J.JMB.2019.10.024
citation: pubmed:31682836
description: A Web Tool for Predicting Stability of Transmembrane α-Helix Association.
feature list: operation_0279
feature list: operation 2415
feature list: operation 3767

TOAST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3170
application sub category: topic 3295
application sub category: topic 3518
citation: S13059-019-1778-0
citation: pmcid:PMC6727351
citation: pubmed:31484546
description: improving reference-free cell composition estimation by cross-cell type differential analysis | Tools for the analysis of heterogeneous tissues | This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities include 1. detect cell-type specific or cross-cell type differential signals 2. improve variable selection in reference-free deconvolution | DNAMethylation, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneTarget, MethylationArray, Microarray, Software
feature list: operation 2495
feature list: operation 3223
feature list: operation 3629
license: GPL-2.0

TOBIAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3170
application sub category: topic 3512
citation: https://doi.org/10.1101/869560
description: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation.
feature list: operation_0337
feature list: operation_0445
feature list: operation 3222
license: MIT
software help: wiki

TOFF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0625
application sub category: topic_0749
application sub category: topic 3300
application sub category: topic 3489
citation: S41597-019-0307-Z
citation: pmcid:PMC6890663
citation: pubmed:31796752
description: database of traits of fish to promote advances in fish aquaculture. toff-project – Database of Traits OF Fish. TOFF (i.e. Traits OF Fish) is a curated database focusing on functional trait information for fish that aims at bringing together behavioral, morphological, phenological, and physiological traits coupled to environmental measurement context into a single open-source access repository. TOFF hosts data from published field and experimental studies. We ultimately aim to provide an inclusive and accessible data resource to facilitate advances in fish research
feature list: operation 3435
feature list: operation 3907

TOPAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3318
application sub category: topic 3384
application sub category: topic 3452
citation: https://doi.org/10.1118/1.4758060
citation: pmcid:PMC3493036
citation: pubmed:23127075
description: Proton Monte Carlo platform for research and clinical applications.
feature list: operation 3629
is accessible for free: true
license: Proprietary
operating system: Linux
operating system: Mac
software help: index.html
primary contact: Joseph Perl

TOPAS-nBio
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2640
application sub category: topic 3314
application sub category: topic 3318
citation: RR15226.1
citation: pmcid:PMC6377808
citation: pubmed:30609382
description: Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology.
is accessible for free: true
operating system: Linux
operating system: Mac
primary contact: Joost Verburg
primary contact: Thomas Bortfeld

TOXcms
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic_0209
application sub category: topic 3172
application sub category: topic 3407
citation: acs.analchem.9b03811
citation: pmcid:PMC7354698
citation: pubmed:31804057
description: Dose-Response Metabolomics to Understand Biochemical Mechanisms and Off-Target Drug Effects with the TOXcms Software. Job opportunities are available
feature list: operation_0490
feature list: operation 3435
feature list: operation 3891

TP-DB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2830
citation: https://doi.org/10.1101/651315
description: Therapeutic Peptide Design DataBase.
feature list: operation 3891
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: guide
primary contact: Chung-Yu Lan
primary contact: Hua-Wen Fu
primary contact: Lee-Wei Yang

TPD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 3050
citation: ECY.2876
citation: pubmed:31471976
description: measuring functional diversity across scales based on TPD with R | Methods for Measuring Functional Diversity Based on Trait Probability Density | Tools to calculate trait probability density functions (TPD) at any scale (e.g. populations, species, communities). TPD functions are used to compute several indices of functional diversity, as well as its partition across scales. These indices constitute a unified framework that incorporates the underlying probabilistic nature of trait distributions into uni- or multidimensional functional trait-based studies. See Carmona et al. (2016) <doi:10.1016/j.tree.2016.02.003> for further information
license: GPL-3.0

TPES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic 3168
citation: btz406
citation: pmcid:PMC6821153
citation: pubmed:31099386
description: Tumor Purity Estimation from SNVs.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: TPES-manual.pdf
primary contact: Alessio Locallo
primary contact: Francesca Demichelis

TPMCalculator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3170
application sub category: topic 3320
application sub category: topic 3512
citation: bty896
description: Software to quantify mRNA abundance of genomic features.
feature list: operation 1812
feature list: operation 2495
feature list: operation 3800
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: wiki
primary contact: David Landsman
primary contact: Leonardo Mariño-Ramírez
primary contact: Lorinc Pongor
primary contact: Roberto Vera Alvarez

TPOT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic_0820
application sub category: topic 3172
application sub category: topic 3474
citation: S00330-021-08228-7
citation: BTZ796
citation: btz470
citation: pmcid:PMC6956793
citation: pmcid:PMC7703753
citation: pubmed:31165141
citation: pubmed:31702773
citation: pubmed:34477909
description: TPOT stands for Tree-based Pipeline Optimization Tool. Consider TPOT your Data Science Assistant. TPOT is a Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.
feature list: operation 3435
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: tpot

Trans-Proteomic Pipeline (TPP)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
additional type: Suite
application sub category: topic_0121
application sub category: topic 3520
citation: pmic.200900375
citation: prca.201400164
citation: 978-1-60761-444-9 15
citation: 978-1-60761-977-2 12
citation: pmcid:PMC3017125
citation: pmcid:PMC4506239
citation: pubmed:20013374
citation: pubmed:20101611
citation: pubmed:21082435
citation: pubmed:25631240
description: Institute for Systems Biology "Trans-Proteomic Pipeline"

TRANSCUP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1101/774315
description: a scalable workflow for predicting cancer of unknown primary based on next-generation transcriptome profiling | Cancer of unknown primary site (CUP) accounts for 5% of all cancer diagnoses. These patients may benefit from more precise treatment when primary cancer site was identified. Advances in high-throughput sequencing have enabled cost-effective sequencing the transcriptome for clinical application. Here, we present a free, scalable and extendable software for CUP predication called TRANSCUP, which enables (1) raw data processing, (2) read mapping, (3) quality report, (4) gene expression quantification, (5) random forest machine learning model building for cancer type clas-sification. TRANSCUP achieved high accuracy, sensitivity and specificity for tumor type classifica-tion based on external RNA-seq datasets. It has potential for broad clinical application for solving the CUP problem
feature list: operation 2495
feature list: operation 3800
license: MIT

TRANSNAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3518
citation: S41598-019-55287-4
citation: pmcid:PMC6908688
citation: pubmed:31831861
description: TRANSNAP is a web database providing comprehensive information on Japanese pear transcriptome.
feature list: operation 2495
feature list: operation 3192
feature list: operation 3672

TRAPeS
type: SoftwareApplication
input: Sequence alignment (nucleic acid)
  type: FormalParameter
  additional type: data 1383
  encoding format: format 2572
output: Sequence report
  type: FormalParameter
  additional type: data 2955
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 2830
citation: gkx615
description: Software for reconstruction of T cell receptors (TCR) using short, paired-end single-cell RNA-sequencing.
feature list: operation_0230
is accessible for free: true
license: Other
operating system: Linux
software help: README.md
primary contact: Shaked Afik

TRAX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3314
application sub category: topic 3393
application sub category: topic 3855
citation: PREPRINTS201911.0114.V1
description: The TRAX Light-Rail Train Air Quality Observation Project. - Department of Atmospheric Sciences. Department of Atmospheric Sciences. College of Mines and Earth Sciences. Monitoring Air Quality Along UTA TRAX Lines.
feature list: operation 2428
feature list: operation 3799

TRC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3172
application sub category: topic 3520
citation: SAGMB-2018-0056
citation: pubmed:31145698
description: Truncated rank correlation (TRC) as a robust measure of test-retest reliability in mass spectrometry data.
feature list: operation 3215
feature list: operation 3633
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://sites.google.com/site/dhyeonyu/trc-manual.pdf
primary contact: Donghyeon Yu

tripr
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2830
citation: s12859-020-03669-1
citation: pmcid:PMC7525938
citation: pubmed:32993478
description: T-cell Receptor/Immunoglobulin Profiler (TRIP)
feature list: operation 2403
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: tripr.pdf
software version: 1.0
primary contact: https://orcid.org/0000-0002-0222-4273

TRITEX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0196
application sub category: topic_0780
application sub category: topic 3673
citation: https://doi.org/10.1101/631648
description: Chromosome-scale sequence assembly of Triticeae genomes with open-source tools.
feature list: operation_0524
feature list: operation_0525
feature list: operation 3216
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: tritexassembly.bitbucket.io
primary contact: Martin Mascher

TRI_tool
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic_0203
application sub category: topic 3557
citation: btw590
description: Web-tool for prediction of protein–protein Interactions in human Transcriptional Regulation.
feature list: operation 2492
feature list: operation 3802
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: tfpred help.php
primary contact: Nevena Veljkovic
primary contact: Vladimir Perovic

TROVE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic 2640
citation: btx600
citation: pubmed:29028982
description: Tool for visualizing and analyzing cancer hallmarks in signaling networks.
feature list: operation 2497
feature list: operation 3562
is accessible for free: true
license: EPL-1.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: TROVE User Guide (Linux).pdf
software help: TROVE User Guide (MacOS).pdf
software help: TROVE User Guide (Win).pdf
primary contact: Huey Eng Chua
primary contact: Sourav S. Bhowmick

TRamWAy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 2229
application sub category: topic 3047
citation: AB5167
citation: pubmed:31765328
description: Mapping spatio-temporal dynamics of single biomolecules in living cells. TRamWAy helps analyzing single molecule dynamics. It infers the diffusivity, drift, force and potential energy across space and time
feature list: operation 2429
feature list: operation 3436

TSDD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0736
application sub category: topic 3512
citation: btw095
description: Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains.
feature list: operation 1812
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Kenneth Watanabe

TSEA-DB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3337
application sub category: topic 3517
citation: GKZ957
citation: pubmed:31680168
description: a trait-tissue association map for human complex traits and diseases. deTSDB, deTS, TSEA, tissue-specificity. TSEA-DB provides a comprehensive reference for trait-associated tissues. A systematic tissue-specific enrichment analysis (TSEA) has been conducted using deTS to infer tissues in which trait-associated genes are enriched. Two reference tissue panels are collected: the GTEx v7 panel (47 tissues) and the ENCODE panel (44 tissues). A total of 5019 GWAS summary statistics data sets for human complex traits and diseases (435 + 161 GWAS data sets from the non-UKBB panel and 4423 data sets from the UKBB panel) have been analyzed for their causal tissues. Content 1. 1. Collection and processing of GWAS summary statistics for complex traits and diseases. The Multi-Trait Collection (MTC) traits were previously reported in the work by Liu et al., 2019
feature list: operation 2428
feature list: operation 2436
feature list: operation 3196
feature list: operation 3232
feature list: operation 3431

TSUNAMI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3170
application sub category: topic 3518
citation: https://doi.org/10.1101/787507
description: Translational Bioinformatics Tool Suite For Network Analysis And Mining. An R software for Gene Co-Expression Analysis. Gene co-expression network (GCN) mining aims to mine gene modules with highly correlated expression profiles across sample cohorts. It may help to reveal latent molecular interactions, identify novel gene functions, pathways and drug targets, as well as providing disease mechanistic insights on for biological researchers. TSUNAMI is developed to allow biological researchers with no programing background to perform GCN mining themselves. Users can get access to our online service from http://spore.ph.iu.edu:3838/zhihuan/TSUNAMI/
feature list: operation 2436
feature list: operation 3463
feature list: operation 3557
feature list: operation 3766

TTAgP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0804
application sub category: topic 2640
citation: J.COMPBIOLCHEM.2019.107103
citation: pubmed:31437642
description: A computational tool for the specific prediction of tumor T cell antigens | Nowadays, cancer is considered a global pandemic and millions of people die every year because this disease remains a challenge for the world scientific community. Even with the efforts made to combat it, there is a growing need to discover and design new drugs and vaccines. Among these alternatives, antitumor peptides are a promising therapeutic solution to reduce the incidence of deaths caused by cancer. In the present study, we developed TTAgP, an accurate bioinformatic tool that uses the random forest algorithm for antitumor peptide predictions, which are presented in the context of MHC class I. The predictive model of TTAgP was trained and validated based on several features of 922 peptides
feature list: operation_0252
feature list: operation 3631

TWOMBLI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic_0769
application sub category: topic 3068
citation: https://doi.org/10.1101/867507
description: A FIJI Macro for quantifying pattern in extracellular matrix. Welcome to The Worklfow Of Matrix BioLogy Informatics (TWOMBLI). Twombli is a Fiji plugin. To get started download the TWOMBLI folder to your computer. Your browser does not support the video tag
feature list: operation 3431
feature list: operation 3435
feature list: operation 3799

TXG-MAPr
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: s00204-021-03141-w
description: In the TXG-MAPr, users can analyze dose- and time-response curves, compound correlation plots and functional annotation of the WGCNA modules to derive mechanistic information of the toxicity. In addition, we included the prediction of transcription factor activities, as well as physical interactions between downstream proteins encoded by the transcriptome, which might be useful in analyzing the perturbations triggered by exposure with toxic compounds. Users can investigate module perturbation of the TG-GATEs compounds by looking at the module eigengene scores (EGS)
feature list: operation 2945

TYGRESS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0611
application sub category: topic 2275
application sub category: topic 3385
application sub category: topic 3452
citation: s41592-019-0651-0
citation: pmcid:PMC7004880
citation: pubmed:31768058
description: In situ structure determination at nanometer resolution using TYGRESS. TYGRESS:Tomography-Guided 3D Reconstruction of Subcellular Structures. Tomography-Guided 3D Reconstruction of Subcellular Structures (TYGRESS) is a hybrid method, which combines the advantageous features of both cryo-electron tomography and single particle cryo-EM to achieve higher resolution than before of complex subcellular structures within their native environment. Back to UT Southwestern Back to UTSW Labs
feature list: operation_0478
feature list: operation 3458

TYGS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0084
application sub category: topic_0637
application sub category: topic 3301
citation: S41467-019-10210-3
citation: gkab902
citation: gkaf1110
citation: pmcid:PMC6522516
citation: pmcid:PMC8728197
citation: pubmed:31097708
citation: pubmed:34634793
citation: pubmed:41160892
description: Automated high-throughput platform for state-of-the-art genome-based taxonomy.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: faqs
primary contact: https://orcid.org/0000-0002-5144-6200

TZMD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0621
application sub category: topic_0637
application sub category: topic 2885
application sub category: topic 3174
citation: S12864-019-6119-X
citation: pmcid:PMC6805505
citation: pubmed:31638897
description: A high-resolution genomic composition-based method with the ability to distinguish similar bacterial organisms. The "tranucleotide-derived Z-value Manhattan Distance” (TZMD) approach profiles genomic composition with high resolution, which can distinguish bacteria at even strain level
feature list: operation_0224
feature list: operation 3196
feature list: operation 3435

TaBSAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Targeted Bisulfite Sequencing Analysis Pipeline A pipeline to analyze the data obtained from targeted bisulfite sequencing through the ion-torrent platform. TaBSAP is a pipeline to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step and enables a researcher to analyze the methylation levels of their samples straight away. It's main features are: -Bisulfite mapping and methylation calling in one single step -Supports single-end read alignments -Alignment seed length, number of mismatches etc. are adjustable -The output gives heatmap with categories.
feature list: operation 3186
feature list: operation 3204
is accessible for free: true
license: MIT
software version: 1.0.0
software version: 1.0.1
software version: 1.0.2

TaF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0160
application sub category: topic_0621
application sub category: topic 3512
citation: s13258-018-0766-1
citation: pubmed:30456524
description: Web platform for taxonomic profile-based fungal gene prediction.
feature list: operation_0476
feature list: operation 3460
feature list: operation 3663
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Theragen Etex Bio Institute

TabSINT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3063
application sub category: topic 3489
citation: https://doi.org/10.1080/14992027.2019.1698776
citation: pubmed:31846397
description: open-source mobile software for distributed studies of hearing. TabSINT is an open source platform for administering tablet based hearing-related exams, as well as general-purpose questionnaires. It is meant to be flexible, easy-to-use, and useful for administrators who manage studies of all sizes. Open source platform for hearing assessments,and general purpose questionnaires

Taba
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic 3474
citation: JCC.26048
citation: pubmed:31410856
description: A Tool to Analyze the Binding Affinity | Taba: Tool to Analyze Binding Affinity | Taba is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. You can use a higher version as well
feature list: operation_0482
feature list: operation 2950

TagGraph
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0121
application sub category: topic_0601
application sub category: topic 3520
citation: s41587-019-0067-5
citation: pmcid:PMC6447449
citation: pubmed:30936560
description: Computational tool that reveals vast protein modification landscapes from large tandem mass spectrometry datasets.
feature list: operation_0417
feature list: operation 3645
feature list: operation 3649

TarHunter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0659
application sub category: topic_0780
citation: btx797
citation: pmcid:PMC6248703
citation: pubmed:29236948
description: Tool for predicting conserved microRNA targets and target mimics in plants.
feature list: operation_0463
feature list: operation 3792
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: README.md
primary contact: Xuan Ma

TargetScanHuman
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3518
application sub category: topic 3519
citation: jcmm.14823
citation: pmcid:PMC6991699
citation: pubmed:31851778
description: Long noncoding RNA ZFAS1 promotes tumorigenesis and metastasis in nasopharyngeal carcinoma by sponging miR-892b to up-regulate LPAR1 expression. Search for predicted microRNA targets in mammals. 1. Select a species Human Mouse Rat Chimpanzee Rhesus Cow Dog Opossum Chicken Frog. 2. Enter a human gene symbol (e.g. "Hmga2"). TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer , 7mer , and 6mer sites that match the seed region of each miRNA.
feature list: operation_0463
feature list: operation 2495
feature list: operation 3223

Target Gene Notebook
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0625
application sub category: topic 3336
citation: https://doi.org/10.1101/757690
description: Connecting genetics and drug discovery | This is the Target Gene Notebook source-code repository | to build TGN backend against git repository:
feature list: operation 3196
license: MIT

TasselNetv2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0780
application sub category: topic 3382
application sub category: topic 3474
citation: S13007-019-0537-2
citation: pmcid:PMC6905110
citation: pubmed:31857821
description: in-field counting of wheat spikes with context-augmented local regression networks. This is the repository for TasselNetv2, presented in:
feature list: operation_0337
feature list: operation 3659
feature list: operation 3799

TaxIt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0781
application sub category: topic 3520
citation: https://doi.org/10.1101/812313
description: An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples.
feature list: operation 3460
feature list: operation 3649
feature list: operation 3767

TcellSubC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0140
application sub category: topic 2229
application sub category: topic 3520
citation: FIMMU.2019.02708
citation: pmcid:PMC6902019
citation: pubmed:31849937
description: An Atlas of the Subcellular Proteome of Human T Cells. This is a curated an in-depth subcellular proteomic map of primary human CD4+ T cells, divided into cytosolic, nuclear and membrane fractions generated by an optimized fractionation and HiRIEF-LC-MS MS workflow for limited amounts of primary cells. The subcellular proteome of T cells was mapped under steady state conditions, as well as upon 15 min and 1 h of T cell receptor (TCR) stimulation, respectively. We quantified the subcellular distribution of 6,572 proteins and identified a subset of 237 potentially translocating proteins, including both well-known examples and novel ones. Microscopic validation confirmed the localization of selected proteins with previously known and unknown localization, respectively.
feature list: operation 2428
feature list: operation 2489
feature list: operation 3630

TeXP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3519
citation: JOURNAL.PCBI.1007293
citation: pmcid:PMC6715295
citation: pubmed:31425522
description: Deconvolving the effects of pervasive and autonomous transcription of transposable elements | TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data | #About TeXP is a pipeline for quantifying abundances of Transposable Elements transcripts from RNA-Seq data. TeXP is based on the assumption that RNA-seq reads overlapping Transposable Elements is a composition of pervasive transcription signal and autonomous transcription of Transposable Elements
feature list: operation_0372
feature list: operation 3233
feature list: operation 3800
license: Apache-2.0

TeachOpenCADD-KNIME
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0209
application sub category: topic_0769
application sub category: topic 2258
application sub category: topic 2840
application sub category: topic 3474
citation: ACS.JCIM.9B00662
citation: pubmed:31612715
description: A Teaching Platform for Computer-Aided Drug Design Using KNIME Workflows.
feature list: operation_0337
feature list: operation 3695
license: CC-BY-4.0

Telescope
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0196
application sub category: topic 3168
citation: bts399
citation: pmcid:PMC3436826
citation: pubmed:22962446
description: Telescope is an open-source web application that tracks the progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. It allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Moreover, output files are rendered in HTML in real time, allowing the use of markdown and rich-text features. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted.
feature list: operation_0310

Telescope
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: JOURNAL.PCBI.1006453
citation: pmcid:PMC6786656
citation: pubmed:31568525
description: Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq. It can be used for Statistical Performance of TE Quantification Methods. All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.
feature list: operation 2495
feature list: operation 3192
feature list: operation 3198
feature list: operation 3800
feature list: operation 3891
license: MIT
software help: telescope demo

TelomereHunter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2640
application sub category: topic 3673
application sub category: topic 3676
citation: s12859-019-2851-0
citation: pmcid:PMC6540518
citation: pubmed:31138115
description: In silico estimation of telomere content and composition from cancer genomes.
feature list: operation 3435
feature list: operation 3798
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: telomerehunter.html
primary contact: Lina Sieverling

TeraPCA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3315
citation: btz157
citation: pubmed:30957838
description: Package to study genetic variation in tera-scale genotypes as it performs PCA of large-scale datasets.
feature list: operation 3196
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

Terminome-seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic_0780
application sub category: topic 3512
application sub category: topic 3542
citation: gkz1059
citation: pmcid:PMC7145512
citation: pubmed:31732725
description: Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. This repository contains data and materials linked to the Terminome-Seq project. The preprint of the manuscript is 2019_Terminome-Seq.pdf or it can be downloaded from the Bioarxiv website here https://www.biorxiv.org/content/10.1101/621938v2
feature list: operation 2441
feature list: operation 2488
feature list: operation 3902

Terra
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0610
application sub category: topic 3316
application sub category: topic 3810
citation: TGIS.12286
citation: pmcid:PMC6764783
citation: pubmed:31565027
description: Terra Populus' Architecture for Integrated Big Geospatial Services | Boundaries are missing for the selected sample geography. Please select a different sample geography

Tersect
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3168
citation: BTZ634
citation: pubmed:31392327
description: a set theoretical utility for exploring sequence variant data | Command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data | Tersect is a command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data. The tool generates index files based on provided variant data (VCF files) which can then be used to rapidly execute flexible set theoretical queries and output the resulting lists of variants in selected regions
feature list: operation 2422
feature list: operation 3196
feature list: operation 3798
license: MIT

Tetrad
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0611
application sub category: topic 2269
citation: https://doi.org/10.1080/10705511.2016.1202771
citation: pmcid:PMC6663104
citation: pubmed:31360055
description: A Set of Stata Commands for Confirmatory Tetrad Analysis | This respository contains three Stata commands for conducting Confirmatory Tetrad Analysis (CTA). In addition, the repository is set up so that the commands can be installed within Stata. Simply type "net install tetrad, from(https://github.com/sbauldry/tetrad/raw/master) replace" without the quotes in Stata's command window. These commands are introduced in Bauldry and Bollen (2016)

ThalPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3315
application sub category: topic 3474
citation: S12911-019-0929-2
citation: pmcid:PMC6836478
citation: pubmed:31699079
description: a web-based prediction tool for discriminating thalassemia trait and iron deficiency anemia. ThalPred: Development of Decision Model for Discriminating Thalassemia Trait and Iron Deficiency Anemia

ThaleMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more.
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 4.3.1-20210109

The Great Genotyper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: The Great Genotyper is an alignment-free population genotyper of small and structural variants. It begins by preprocessing raw sequencing data to create a Counting Colored De Bruijn Graph (CCDG). Then it uses the succinct CCDG to genotype any list of phased or unphased variants, leveraging the population information to increase both precision and recall. The Great Genotyper offers the same accuracy as the state-of-the-art with unprecedented performance. It took 100 hours to genotype 4.5M variants in 4.2K whole genome human samples using one server with 32 cores and 145GB of memory.

The Ark
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0607
application sub category: topic 3063
application sub category: topic 3071
citation: btw675
citation: pubmed:28003258
description: Web-based data management tool for health and medical research.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation
primary contact: Adrian Bickerstaffe

TheoReTS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0593
application sub category: topic 3307
application sub category: topic 3318
citation: https://doi.org/10.1063/1.5096883
citation: pubmed:31117786
description: Theoretical Reims-Tomsk Spectral data.
feature list: operation_0386
feature list: operation_0476
feature list: operation 3860
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: home.help
primary contact: Andrei Nikitin
primary contact: Michael Rey
primary contact: Vladimir G. Tyuterev

Thera-SAbDab
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0154
citation: gkz827
citation: pmcid:PMC6943036
citation: pubmed:31555805
description: the Therapeutic Structural Antibody Database | The Structural Antibody Database | (Therapeutic Structural Antibody Database) | Thera-SAbDab paper: Raybould, M.I.J., Marks, C. et al (2019). Nucleic Acids Res. gkz827 [link] | SAbDab paper: Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146 [link]
feature list: operation_0279
feature list: operation 2518
feature list: operation 3095

ThermoLabAnimal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic 3382
application sub category: topic 3500
citation: J.PHYSBEH.2019.05.004
citation: pubmed:31078672
description: High-throughput analysis software for non-invasive thermal assessment of laboratory mic.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Paulo Aguiar

ThermoNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0097
application sub category: topic 3474
application sub category: topic 3794
citation: JOURNAL.PCBI.1007283
citation: pmcid:PMC6752863
citation: pubmed:31483777
description: Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction | This is a TensorFlow implementation accompanying our paper. This codebase is based on Shreshthgandhi's Tensorflow implementation of the cdeepbind model. The framework of model training and testing have beed adopted with minor changes. Other code files have been modified and re-structured with changes specific to our model. And the folder, scripts/RNAsubopt is a copy of RNAsubopt from the ViennaRNA project | We used two datasets to evaluate our model. The following datsets were used for training our models | You can download the datasets from the corresponding website. After that, you should prepare the data used in the training code according to the steps below. We use the CLIP-seq dataset as an example | BTW, The ThermoNet implementation is available at invitro bin deepbind_model utils_update.py
feature list: operation_0278
feature list: operation 3901
feature list: operation 3902

ThermoRawFileParser
type: SoftwareApplication
input: Mass spectrum
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3712
output: Mass spectrum
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3244
  encoding format: format 3651
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic 3172
application sub category: topic 3520
citation: https://doi.org/10.1101/622852
description: Open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML
feature list: operation 3215
feature list: operation 3434
feature list: operation 3695
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Computational Omics and Systems Biology Group

Thesaurus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0602
application sub category: topic 3520
citation: s41592-019-0498-4
citation: pmcid:PMC7012383
citation: pubmed:31363206
description: quantifying phosphopeptide positional isomers | The human phosphorylation regulatory network represents a complex signaling cascade where proteins can be phosphorylated at multiple sites resulting in different functional states. Here we present Thesaurus, a hybrid search engine that detects, localizes, and quantifies novel positional isomers using site-specific fragment ions directly from data independent acquisition mass spectrometry experiments. This software works for several PTMs in addition to phosphorylation. Check out our paper describing Thesaurus and what it can do at Nature Methods (Searle et al, 2019)!
feature list: operation_0417
feature list: operation 3216
feature list: operation 3629

Thor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3382
citation: V1
citation: pmcid:PMC11952649
citation: pubmed:40162205
description: Spatial transcriptomics integrates transcriptomics data with histological tissue images, offering deeper insights into cellular organization and molecular functions. However, existing computational platforms mainly focus on genomic analysis, leaving a gap in the seamless integration of genomic and imaging modalities. Thor is a comprehensive spatial transcriptomics analysis tool designed to bridge this gap by enabling efficient co-analysis of gene expression profiles and high-resolution tissue images. It provides scalable workflows for spatial feature extraction, cell segmentation, gene–spatial correlation, and visualization, facilitating multi-omic insights into tissue architecture and cellular heterogeneity.
feature list: operation_0314
feature list: operation_0337
feature list: operation 3557
feature list: operation 3891
software help: thor

Threshold-seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic 3170
citation: btx073
citation: pmcid:PMC5870860
citation: pubmed:28203700
description: Tool for determining the threshold in short RNA-seq datasets.
feature list: operation 3192
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Isidore Rigoutsos

Tibanna
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0769
citation: btz379
citation: pmcid:PMC6931271
citation: pubmed:31077294
description: Software for scalable execution of portable pipelines on the cloud.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest
primary contact: Burak H. Alver
primary contact: Peter J. Park

TideHunter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0749
application sub category: topic 2885
citation: BTZ376
citation: pmcid:PMC6612900
citation: pubmed:31510677
description: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain | TideHunter is an efficient and sensitive tandem repeat detection and consensus calling tool which is designed for tandemly repeated long-read sequence (INC-seq, R2C2, NanoAmpli-Seq)
feature list: operation 3192
feature list: operation 3195
feature list: operation 3798
license: GPL-3.0

Time-energy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3077
application sub category: topic 3277
application sub category: topic 3678
citation: J.DIB.2019.104670
citation: pmcid:PMC6833352
citation: pubmed:31709289
description: Time-energy measured data on modern multicore systems running shared-memory applications.

Tn-seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0798
application sub category: topic 3168
application sub category: topic 3386
citation: 978-1-4939-9849-4 12
citation: pubmed:31523773
description: Scripts for analyzing transposon sequencing data used by the Whiteley lab | Custom scripts for analyzing (parsing, mapping, and tallying) Tn-seq reads and determining differentially abundant transposon insertion mutants | The scripts contained herein can be used to automatically analyze high-throughput (Illumina) sequencing reads derived from transposon-genome junctions
feature list: operation 1812
feature list: operation 3192
feature list: operation 3461

TogoGenome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0089
application sub category: topic_0625
application sub category: topic_0637
citation: bay132
citation: pmcid:PMC6323299
citation: pubmed:30624651
description: Genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches.
feature list: operation_0224
feature list: operation_0337
feature list: operation 3431
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Keita Urashima

TogoStanza
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic_0637
application sub category: topic 3489
citation: bay132
citation: pmcid:PMC6323299
citation: pubmed:30624651
description: Generic Web framework for rendering an information block.
feature list: operation_0224
feature list: operation_0337
feature list: operation 3431
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: faq
software help: Getting-Started.md
software help: Reference.md
primary contact: Keita Urashima

Tomato Genome Browser
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0622
citation: 1471-2105-9-s2-s7
citation: pmcid:PMC2323670
citation: pubmed:18387209
description: Genome browser for tomato (cultivar Heinz 1706 version 2.50) that includes RNAseq tags, EST and Tentative Consensus sequences to investigate the functional and structural annotation of the tomato genome.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: general help.html
software version: 1

Top-Down Garbage Collector
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic 3520
citation: btz085
citation: pubmed:30715205
description: Tool for selecting high-quality top-down proteomics mass spectra.
feature list: operation 3627
feature list: operation 3637
feature list: operation 3801
is accessible for free: true
license: Unlicense
operating system: Windows
software help: Work.html
primary contact: Diogo B. Lima
primary contact: Julia Chamot-Rooke
primary contact: Paulo C. Carvalho

Topaz
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3382
application sub category: topic 3474
citation: S41592-019-0575-8
citation: pmcid:PMC6858545
citation: pubmed:31591578
description: A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph denoising using deep denoising models.
feature list: operation 2422
feature list: operation 3435
feature list: operation 3458
license: GPL-3.0

Topaz-Denoise
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic 3382
application sub category: topic 3474
citation: https://doi.org/10.1101/838920
description: A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph denoising using deep denoising models.
feature list: operation_0302
feature list: operation 3458
feature list: operation 3891
license: GPL-3.0

Topconfects
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3518
citation: s13059-019-1674-7
citation: pmcid:PMC6437914
citation: pubmed:30922379
description: R package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list.
feature list: operation 3223
feature list: operation 3680
feature list: operation 3800
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
operating system: Windows
software help: topconfects
software version: 1.0.0

Topological Tumor Graphs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3308
citation: 0008-5472.can-19-2268
citation: pmcid:PMC7985597
citation: pubmed:31874858
description: a graph-based spatial model to infer stromal recruitment for immunosuppression in melanoma histology. Topological-tumour-graphs
feature list: operation 3432
feature list: operation 3557
feature list: operation 3659

ToulligQC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: A post sequencing QC tool for Oxford Nanopore sequencers.
feature list: operation 3218

Tox21
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0593
application sub category: topic 3343
citation: EHP5314
citation: pmcid:PMC6792352
citation: pubmed:31566444
description: > LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'agonist', 'RXR' | Limited Chemical Structural Diversity Found to Modulate Thyroid Hormone Receptor in the Tox21 Chemical Library | Concentration 5-30% of expected value
feature list: operation 3642

TraceMontage
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3382
citation: j.jneumeth.2019.108560
citation: pmcid:PMC6950642
citation: pubmed:31874186
description: A method for merging multiple independent neuronal traces.
feature list: operation 3552

Track-Control
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3382
application sub category: topic 3421
citation: https://doi.org/10.1101/2019.12.11.873372
description: Track-Control is an automatic video-based real-time closed-loop behavioral control toolbox.

TrackFind
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
additional type: Web API
additional type: Web service
application sub category: topic_0089
application sub category: topic_0091
application sub category: topic 3071
citation: f1000research.1117098.1
description: TrackFind is a FAIR genomic tracks search and curation engine. It supports crawling of the TrackHub Registry and other data portals to fetch track metadata. Crawled metadata can be accessed through hierarchical browsing or by search queries, both through a web-based user interface and as a RESTful API. TrackFind supports advanced SQL-based search queries that can be easily built in the user interface, and the search results can be browsed and exported in JSON or GSuite format. The RESTful API allows downstream tools and scripts to easily integrate TrackFind search, currently demonstrated by the GSuite HyperBrowser and EPICO.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Dmytro Titov
primary contact: Eivind Hovig

TractaViewer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0659
application sub category: topic 3377
citation: btz270
citation: pubmed:31070721
description: Genome-wide tool for preliminary assessment of therapeutic target druggability.
feature list: operation_0337
feature list: operation 2422
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Neil Pearson

TractoFlow
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 3384
application sub category: topic 3444
citation: j.neuroimage.2020.116889
citation: https://doi.org/10.1101/631952
citation: pubmed:32447016
description: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity | Files needed to build a Singularity container to run the TractoFlow pipeline | Singularity related files for TractoFlow | The TractoFlow pipeline is a fully automated and reproducible dMRI processing pipeline. TractoFlow takes raw DWI, b-values, b-vectors, T1 weighted image (and a reversed phase encoded b=0 if available) to process DTI, fODF metrics and a whole brain tractogram
feature list: operation 3435
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: latest

Trainable Weka Segmentation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3068
application sub category: topic 3382
application sub category: topic 3474
citation: btx180
citation: pubmed:28369169
description: Machine learning tool for microscopy pixel classification.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Trainable Weka Segmentation
software version: 3.2.33
primary contact: Ignacio Arganda-Carreras

Trans-NanoSim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: https://doi.org/10.1101/800110
description: NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology. The second version of NanoSim (v2.0.0) uses minimap2 as default aligner to align long genomic ONT reads to reference genome. It leads to much faster alignment step and reduces the overall runtime of NanoSim. We also utilize HTSeq, a python package, to read SAM alignment files efficiently.
feature list: operation_0335
feature list: operation 3185
feature list: operation 3198
feature list: operation 3258

TransDecoder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic_0622
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3673
description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
feature list: operation_0436
feature list: operation_0524
feature list: operation 3644

TransLiG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3170
application sub category: topic 3308
citation: s13059-019-1690-7
citation: pmcid:PMC6480747
citation: pubmed:31014374
description: De novo transcriptome assembler that uses line graph iteration.
feature list: operation_0524
feature list: operation 3258
feature list: operation 3644
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac

TransPrise
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3168
application sub category: topic 3474
citation: PEERJ.7990
citation: pmcid:PMC6827441
citation: pubmed:31695967
description: a novel machine learning approach for eukaryotic promoter prediction. Approach for prediction of eukaryotic transcription start sites. A deep learning approach for precise prediction of eukaryotic transcription start sites. Our approach offers significant improvement over existing promoter prediction methods. We provide the full basis for the comparison and encourage users to freely access our computational method to facilitate and streamline their own analyses. ./data/ contains some data files. TSS_MSU.txt was used for TSS sequence taking. Rice genome can be downloaded from MSU rice experiment official page
feature list: operation_0440
feature list: operation 3196
feature list: operation 3659
feature list: operation 3663
license: GPL-2.0

Transcriptologs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0084
citation: https://doi.org/10.1177/1177932217690136
citation: pmcid:PMC5348085
citation: pubmed:28469416
description: Software for the prediction of orthologs between two species, based on transcripts sequence similarities. A procedure to extend BLAST alignments and to define orthologs based on the “Bidirectional Best Hit” approach was implemented.
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Luca Ambrosino

Transformer-CNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2258
application sub category: topic 3382
application sub category: topic 3474
citation: CHEMRXIV.9961787.V1
description: Fast and Reliable Tool for QSAR. Transformer CNN for QSAR/QSPR modelling. The repository contains the source code for a new Transformer-CNN method described in our paper http://arxiv.org/abs/1911.06603. First, we trained the Transformer model on SMILES canonicalization task, e.g., given an arbitrary SMILES, the model converts it to a canonical one. Second, we use the internal representation of the Transformer (the output of the encoding stack with shape (BATCH, LENGTH, EMBEDDING)) as SMILES embeddings and build upon them CharNN model (Convolution and HighWay as it is done in DeepChem). The resulting model works both in classification and regression settings
feature list: operation 3659

Transition Scale-Spaces
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
citation: NECO A 01255
citation: pubmed:31835003
description: A Computational Theory for the Discretized Entorhinal Cortex.
feature list: operation 2422
license: MIT

Transitivity
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0821
application sub category: topic 3314
application sub category: topic 3512
citation: molecules24193478
citation: pmcid:PMC6803931
citation: pubmed:31557893
description: A Code for Computing Kinetic and Related Parameters in Chemical Transformations and Transport Phenomena | Recent advances in phenomenological descriptions of the kinetics of rate processes (Aquilanti et al., 2010, 2017, 2018) motivated this code based on detailed formulations given in previous works | Theoretical and Computational Chemistry
feature list: operation_0334
feature list: operation_0337
feature list: operation 3891

Transposons
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0749
application sub category: topic_0798
application sub category: topic 3512
citation: S41598-019-43403-3
citation: pmcid:PMC6510757
citation: pubmed:31076573
description: Recognition of 3′-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models.
feature list: operation_0427
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Maria Poptsova

Tree-Weighting
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3474
citation: pmcid:PMC6980320
citation: pubmed:31797618
description: Tree-Weighting for Multi-Study Ensemble Learners.

TreeCluster
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3293
application sub category: topic 3305
citation: JOURNAL.PONE.0221068
citation: pmcid:PMC6705769
citation: pubmed:31437182
description: Clustering biological sequences using phylogenetic trees | Efficient phylogenetic clustering of viral sequences | TreeCluster is a tool that, given a tree T (Newick format) and a distance threshold t, finds the minimum number of clusters of the leaves of T such that some user-specified constraint is met in each cluster. The user can also specify a branch support threshold s such that no pair of leaves in any cluster can be connected by branches with support less than or equal to s. Note that all leaves given a cluster of -1 are singletons, meaning they did not cluster with any other leaves (i.e., each leaf with a cluster of -1 is in its own cluster)
feature list: operation_0546
feature list: operation_0557
feature list: operation 3478
license: GPL-3.0

TreeExp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3293
citation: BTZ405
citation: pubmed:31114853
description: R package that performs analyses of expression evolution from RNA-seq data, including optimized input formatting, normalization and pair-wise distance evaluation, expression character tree inference and preliminary phylogenetic network analysis.
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: TreeExp-Tutorial
primary contact: Hang Ruan
primary contact: Xun Gu

TreeFix-TP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic 3168
application sub category: topic 3301
application sub category: topic 3305
application sub category: topic 3324
citation: https://doi.org/10.1101/813931
description: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference. Computational Biology Research Laboratory. TreeFix-TP is a program for reconstructing highly accurate transmission phylogenies, i.e., phylogenies depicting the evolutionary relationships between infectious disease strains (viral or bacterial) transmitted between different hosts. TreeFix-TP is designed for scenarios where multiple strain ... Our websites may use cookies to personalize and enhance your experience. By continuing without changing your cookie settings, you agree to this collection. For more information, please see our University Websites Privacy Notice . TreeFix-TP is a program for reconstructing highly accurate transmission phylogenies, i.e., phylogenies depicting the evolutionary relationships between infectious disease strains (viral or bacterial) transmitted between different hosts
feature list: operation_0540
feature list: operation_0547
feature list: operation 3478

TreeMerge
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0194
application sub category: topic 3512
citation: BTZ344
citation: pmcid:PMC6612878
citation: pubmed:31510668
description: a new method for improving the scalability of species tree estimation methods | TreeMerge is a tool for scaling phylogengy estimation methods to large datasets. TreeMerge can be used in a divide-and-conquer framework as follows: 1) divide the species set into disjoint subsets, 2) construct trees on each subset, and 3) combine the subset trees using an associated distance matrix (on the full species set). TreeMerge has been sucessfully tested in the context of species tree estimation (Molloy and Warnow, 2019)
feature list: operation_0544
feature list: operation_0547
feature list: operation_0555

Treerecs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0623
application sub category: topic 3293
citation: https://doi.org/10.1101/782946
description: Treerecs is an open-source (species- and gene-) tree reconciliation software distributed under the GNU AGPL licence.
feature list: operation_0323
feature list: operation_0326
feature list: operation_0492
license: AGPL-3.0

TreeshrewDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic 3500
citation: J.ISSN.2095-8137.2019.063
citation: pubmed:31418539
description: > CORRECT NAME OF TOOL COULD ALSO BE 'TreeshrewDB v2.0' | Chromosomal level assembly and population sequencing of the Chinese tree shrew genome | Symbol Accession number Full gene name | &nbspFan Y, Yu D et al., 2014. Tree shrew database (TreeshrewDB): a knowledge base for Chinese tree shrew genome biology. Scientific Reports, 4: 7145 | 2019-09-05 Upgrading, some functions are not available
feature list: operation_0484
feature list: operation_0525
feature list: operation 3216

TriPOINT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic_0659
citation: bty998
citation: pmcid:PMC6662310
citation: pubmed:30566622
description: Software tool to prioritize important genes in pathways and their non-coding regulators.
feature list: operation_0533
feature list: operation 3223
feature list: operation 3501
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: UserManual.pdf
primary contact: Asa Thibodeau

Trimitomics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3170
application sub category: topic 3308
citation: https://doi.org/10.1111/1755-0998.13033
citation: pubmed:31070854
description: Efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species.
feature list: operation_0525
feature list: operation 3192
feature list: operation 3258
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Ana Riesgo
primary contact: Bruna Plese

Tripal MapViewer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 3489
citation: BAZ100
citation: pmcid:PMC6829499
citation: pubmed:31688940
description: A tool for interactive visualization and comparison of genetic maps. Tripal is an open-source, resource-efficient toolkit for construction of genomic, genetic and breeding databases. It facilitates development of biological websites by providing tools to integrate and display biological data using the generic database schema, Chado, together with Drupal, a popular website creation and content management system. Tripal MapViewer is a new interactive tool for visualizing genetic map data. Developed as a Tripal replacement for Comparative Map Viewer (CMap), it enables visualization of entire maps or linkage groups and features such as molecular markers, quantitative trait loci (QTLs) and heritable phenotypic markers. It also provides graphical comparison of maps sharing the same markers as well as dot plot and correspondence matrices
feature list: operation_0282
feature list: operation_0490
feature list: operation 2421

TropGeneDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 3810
description: TropGeneDB is a database that manages genomic, genetic and phenotypic information about tropical crops. It is organised on a crop basis.

Tulip
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3169
application sub category: topic 3173
application sub category: topic 3512
citation: https://doi.org/10.1101/624486
description: Toolkit for rapidly simulating ChIP-seq data using statistical models of the experimental steps.
feature list: operation 3222
feature list: operation 3798
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: An Zheng

TumorCNV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0160
application sub category: topic_0625
application sub category: topic 3673
citation: BTZ429
citation: pubmed:31125057
description: Joint detection of germline and somatic copy number events in matched tumor-normal sample pairs.
feature list: operation 3196
feature list: operation 3233
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Yongzhuang Liu

TupaiaBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: S41598-019-48867-X
citation: pmcid:PMC6710255
citation: pubmed:31451757
description: Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing | Tupaia belangeri (Family Tupaia, Genus Tupaia) | Tupaia ( Tupaia belangeri ) is a small mammal belonging to the family Tupaiidae, which consists of four genera and 19 extant species. The members of the genus Tupaia , which are colloquially referred to as the tree shrews, were first recorded in a sketch by William Ellis on a voyage with Captain Cook in 1780. Tree shrews are similar in appearance to squirrels, and their body weight ranges between 120-200 g. The natural habitat of the tree shrews consists of the tropical rainforests in South East Asia, where they feed on fruits, insects, and small vertebrates
feature list: operation 2495
feature list: operation 3216
feature list: operation 3501

Tutorial: MD Setup
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Protein MD Setup tutorial using BioExcel Building Blocks - a Jupyter Notebook tutorial.

TwinsUK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3305
application sub category: topic 3399
application sub category: topic 3697
citation: THG.2019.65
citation: pubmed:31526404
description: The UK Adult Twin Registry Update | If you would like access to data or samples from the Department Of Twin Research & Genetic Epidemiology or are interested in proposing a collaboration with us, please first follow the link DTR Policy Document for data access which will give you the necessary background information | You will then need to complete a “Data Access Proposal Form” (links below) and email the completed form to the Data Access Manager Victoria Vazquez or fax to +44 (0)20 7188 6718 for consideration by the Department of Twin Research Executive Committee | No attempt should be made to link or combine the data provided under this agreement to other information or archived data available for the data sets provided, even if access to that data has been formally granted to you, or it is freely available without restriction, unless specific permission to do so has been received from the TwinsUK TREC | The proposal should specify the data and or samples required clearly

TypeTE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3170
application sub category: topic 3295
application sub category: topic 3673
citation: https://doi.org/10.1101/791665
description: a tool to genotype mobile element insertions from whole genome resequencing data. Genotyping of segregating mobile elements insertions. This pipeline is developped by Jainy Thomas (University of Utah) and Clement Goubert (Cornell University). Elaborated with the collaboration of Jeffrey M. Kidd (University of Michigan). TypeTE is a pipeline dedicated to genotype segregating Mobile Element Insertion (MEI) previously scored with a MEI detection tool such as MELT (Mobile Element Locator Tool, Gardner et al., 2017). Please adress all you questions and comments using the "issue" tab of the repository
feature list: operation 3183
feature list: operation 3196
feature list: operation 3227

U-PASS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3517
citation: BTZ637
citation: pubmed:31400194
description: > CORRECT NAME OF TOOL COULD ALSO BE 'IMPLEMENTATION:U-PASS' | unified power analysis and forensics for qualitative traits in genetic association studies | GWAS power calculator / generic power calculations for large scale association tests. Built with R Shiny | U-PASS: a Unified Power Analysis of Association Studies
feature list: operation 3659
license: MIT

UALCAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3512
citation: j.neo.2017.05.002
citation: pmcid:PMC5516091
citation: pubmed:28732212
description: Comprehensive, user-friendly, and interactive web resource for analyzing cancer OMICS data.
feature list: operation 2436
feature list: operation 3463
feature list: operation 3766
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: ualcan.path.uab.edu
software help: tutorial.html

UniBioDicts
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
additional type: Database portal
additional type: Suite
application sub category: topic_0091
application sub category: topic 3071
description: Unified Biological Dictionaries (UniBioDicts) is a set of software packages that unite many of the most important biological controlled vocabularies, database vocabularies, and ontologies, under a common query-interface. These packages can access these disparate biological resources, and map their vocabulary data onto a common representation consisting of terms (which biocurators prefer to use), a unique identifier (which computers can reason with), and various descriptive metadata. This cross-resource infrastructure is essential for an efficient, modernized biocuration process, as it directly enables the autocomplete-based curation of particularly context-rich annotations, that combine terminology from across biological niches.
feature list: operation_0224
is accessible for free: true
license: AGPL-3.0

UCSC Genome Browser Utilities
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0080
description: Utilities for handling sequences and assemblies from the UCSC Genome Browser project.
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

UGICR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3305
application sub category: topic 3412
application sub category: topic 3421
citation: BMJOPEN-2019-031434
citation: pmcid:PMC6773358
citation: pubmed:31575580
description: The Upper Gastrointestinal Cancer Registry (UGICR) is a clinical quality registry, that collects information about the diagnosis, treatment and outcomes of individuals with upper gastrointestinal cancer. The registry is managed by the Cancer Research Program part of Public Health and Preventive Medicine , Monash University.
feature list: operation 3454

ULTRA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0157
application sub category: topic_0749
application sub category: topic 2885
citation: https://doi.org/10.1145/3233547.3233604
citation: pmcid:PMC6508075
citation: pubmed:31080962
description: > MEDIUM CONFIDENCE! | A Model Based Tool to Detect Tandem Repeats | ULTRA Locates Tandemly Repetitive Areas | To contribute to ULTRA development, you want to be on the develop branch, which is where we are currently integrating feature branches. For more information, see the ULTRA wiki
feature list: operation_0368
feature list: operation_0452
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Daniel Olson

UMI-VarCal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic 3120
application sub category: topic 3168
citation: https://doi.org/10.1101/775817
description: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries | UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries
feature list: operation_0232
feature list: operation 3225
feature list: operation 3227
license: MIT

UNCOVER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3336
citation: JOURNAL.PCBI.1006802
citation: pmcid:PMC6550413
citation: pubmed:31120875
description: Efficient algorithms to discover alterations with complementary functional association in cancer.
feature list: operation 3219
feature list: operation 3501
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0003-2244-2320

UNCeqR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3170
citation: gku489
citation: pmcid:PMC4117748
citation: pubmed:24970867
description: Method and associated software for discovering somatic mutations using the integration of DNA and RNA sequencing.
feature list: operation_0452
feature list: operation 3196
feature list: operation 3227
is accessible for free: true
license: MIT
operating system: Linux
software help: README.md
primary contact: Matt Wilkerson

UNI-EM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 2229
application sub category: topic 3382
application sub category: topic 3474
citation: S41598-019-55431-0
citation: pmcid:PMC6923391
citation: pubmed:31857624
description: An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images. A unified environment for DNN-based automated segmentation of neuronal EM images. Check the following pages after installation. Click the link "main.exe" in [UNI-EM] to launch the control panel. Urakubo, H., Bullmann, T., Kubota, Y., Oba, S., Ishii, S., UNI-EM: An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images. Scientific Reports 9, 19413 (2019) doi:10.1038/s41598-019-55431-0
license: GPL-3.0

UNIPred-Web
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 1775
application sub category: topic 3518
citation: S12859-019-2959-2
citation: pmcid:PMC6694573
citation: pubmed:31412768
description: a web tool for the integration and visualization of biomolecular networks for protein function prediction | In order to execute an experiment, you must first create an experiment design | {{ experiment.name }}-{{ experiment.newid }}
feature list: operation 1777
feature list: operation 3083
feature list: operation 3439

UNRAVEL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3335
application sub category: topic 3337
application sub category: topic 3384
citation: s12471-019-1288-4
citation: pmcid:PMC6712144
citation: pubmed:31134468
description: Big data analytics research data platform to improve care of patients with cardiomyopathies using routine electronic health records and standardized biobanking.
feature list: operation_0306
feature list: operation 3435
feature list: operation 3501
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://www.unravelrdp.nl/

UNet++
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0611
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3452
application sub category: topic 3474
citation: tmi.2019.2959609
citation: pmcid:PMC7357299
citation: pubmed:31841402
description: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation. Official Keras Implementation for UNet++ in IEEE Transactions on Medical Imaging and DLMIA 2018. UNet++: A Nested U-Net Architecture for Medical Image Segmentation. UNet++ is a new general purpose image segmentation architecture for more accurate image segmentation. UNet++ consists of U-Nets of varying depths whose decoders are densely connected at the same resolution via the redesigned skip pathways, which aim to address two key challenges of the U-Net: 1) unknown depth of the optimal architecture and 2) the unnecessarily restrictive design of skip connections
feature list: operation_0479
feature list: operation 3436
license: MIT

UOVOS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0176
application sub category: topic 3382
application sub category: topic 3474
citation: TIP.2019.2930152
citation: pubmed:31369377
description: Unsupervised Online Video Object Segmentation With Motion Property Understanding | Tao Zhuo, Zhiyong Cheng, Peng Zhang, Yongkang Wong, and Mohan Kankanhalli | Results on DAVIS-2016 TrainVal Dataset (50 videos)
feature list: operation 2939
feature list: operation 3891

UPCLASS
type: SoftwareApplication
input: UniProt accession
  type: FormalParameter
  additional type: data 3021
input: Pathway or network
  type: FormalParameter
  additional type: data 2600
input: Report
  type: FormalParameter
  additional type: data 2048
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3474
description: A Convolution Neural Network (CNN) model to classify publications with accession annotations according to UniProtKB categories
feature list: operation 3927

UPObase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0160
application sub category: topic_0621
application sub category: topic_0637
application sub category: topic_0821
application sub category: topic 3293
citation: BAZ122
citation: pmcid:PMC6902001
citation: pubmed:31820805
description: an online database of unspecific peroxygenases. UPObase: Unspecific Peroxygenase Database : Homepage. Unspecific Peroxygenase Database (UPObase) is a genome mining pipeline based database which consists of all the sequences of fungal unspecific peroxygenases (UPOs) present in the fungal kingdom. The fungal UPOs in this database are obtained by searching against all the fungal genomes present in the Ensembl database. This server uses profile hidden Markov models (HMMs) for homology search and incorporates clustering algorithms to group the most similar sequences
feature list: operation_0239
feature list: operation 2421
feature list: operation 2995
feature list: operation 3092
feature list: operation 3431

URCFG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic 2229
application sub category: topic 3382
citation: G3.119.400541
citation: pmcid:PMC6829132
citation: pubmed:31690598
description: Expression-Based Cell Lineage Analysis in Drosophila Through a Course-Based Research Experience for Early Undergraduates.
feature list: operation 2421
feature list: operation 3463

US200 CN200
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0605
application sub category: topic 3384
application sub category: topic 3444
citation: j.neuroimage.2019.116318
citation: pmcid:PMC6980905
citation: pubmed:31689538
description: Sample sizes and population differences in brain template construction. Caucasian and Chinese Brain templates [US200 CN200]
feature list: operation 3435

UT-Heart
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0202
application sub category: topic 3335
application sub category: topic 3379
citation: KJPP.2019.23.5.295
citation: pmcid:PMC6717797
citation: pubmed:31496866
description: Clinical and pharmacological application of multiscale multiphysics heart simulator, UT-Heart | Cardiotoxicity Hazard Map/ECG Data Base NEW | The world’s leading technologies open the new door for:
feature list: operation 2426

UTAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3170
application sub category: topic 3308
citation: s12859-019-2728-2
citation: pmcid:PMC6434621
citation: pubmed:30909881
description: User-friendly Transcriptome Analysis Pipeline.(UTAP) is open source, web-based intuitive platform available to the biomedical research community, enabling researchers to efficiently and accurately analyse transcriptome sequence data.
feature list: operation 3223
feature list: operation 3680
feature list: operation 3800
is accessible for free: true
operating system: Linux
software help: utap
primary contact: Refael Kohen

UTRome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3170
application sub category: topic 3512
citation: GR.254839.119
citation: pmcid:PMC6886508
citation: pubmed:31744903
description: The C. elegans 3' UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3'-UTR biology, and miRNA targeting. The UTRome.org database is intended as a comprehensive resource for 3'UTR biology in C. elegans . The database provides detailed information on 3'UTR structures and alternative polyadenylation for all protein-coding mRNAs, and includes annotations extracted from other databases (such as WormBase and PicTar ) as well as new annotations generated by others. 3'UTRs are important portions of mRNAs required for post-transcriptional regulation by interacting with proteins or non-coding RNAs (e.g. microRNAs). To study the role of 3'UTRs we are building a 3'UTR database for C. elegans .
feature list: operation_0428
feature list: operation_0463
feature list: operation 3792

UVP
type: SoftwareApplication
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1930
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0622
application sub category: topic 3301
author: https://orcid.org/0000-0003-1064-6895
citation: s41598-018-33731-1
citation: pmcid:PMC6194142
citation: pubmed:30337678
description: The Unified Variant Pipeline (UVP) is used to identify variants and assign lineage from Mycobacterium tuberculosis sequence data.
feature list: operation 3198
feature list: operation 3227
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software version: 2.6.0
software version: 2.7.0

Ularcirc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3320
application sub category: topic 3512
citation: gkz718
citation: pmcid:PMC6846653
citation: pubmed:31435647
description: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing | An R-shiny app that provides backsplice and canonical splicing analysis for both circRNA and parental transcripts | An R package that provides analysis and visualisation of canonical and backsplice junctions. Takes output provided by the STAR aligner as well as CIRI2 and circExplorer2 output and enables circRNA downstream analysis | Ularcirc manuscript now available through Nucleic Acids Research | Author and maintainer: David Humphreys (d.humphreys at victorchang dot edu dot au) | Ularcirc can annotate circRNA with overlapping gene information. This is obtained from available bioconductor databases. Use the following command to identify what databases to download:
feature list: operation_0337
license: GPL-3.0

Umbria
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
citation: PEERJ.PREPRINTS.2096V2
description: Geothematic open data in Umbria region. Carta di pericolosità sismica locale dell’Umbria. Benvenuti nel Portale Open Data dell' Umbria. I dati della Pubblica Amministrazione umbra a disposizione dei cittadini. www.regione.umbria.it leggi di più. La cartografia di pericolosità sismica vettoriale della Regione Umbria è stata ultimata nel 2013 utilizzando tutti gli originali d'autore delle carte di pericolosità sismica locale realizzate alla scala 1:10.000, riviste ed omogeneizzate
feature list: operation 3891

UniRep
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0130
application sub category: topic_0605
application sub category: topic 3306
application sub category: topic 3474
application sub category: topic 3895
citation: s41592-019-0598-1
citation: pmcid:PMC7067682
citation: pubmed:31636460
description: Unified rational protein engineering with sequence-based deep representation learning. UniRep model, usage, and examples. UniRep, a mLSTM "babbler" deep representation learner for protein engineering informatics. Analysis and figure code from Alley et al. 2019. git clone https://github.com/churchlab/UniRep-analysis.git. First clone or fork this repository and navigate to the repository's top directory (cd UniRep). We recommend using our docker environments. Install docker to get started
feature list: operation_0476
feature list: operation 1777
feature list: operation 3630

Unicorn Papers
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Library
application sub category: topic_0605
application sub category: topic 3068
application sub category: topic 3316
application sub category: topic 3473
description: Top ‱ cited papers from PUBMED. Unicorn Papers are based on an equal contribution (EC) citation model in which the total number of citations had been divided by the number of the authors. Currently, the list contains 3405 papers with ECcit ≥ 847.0 (updated monthly since 2020). ‱ - permyriad, literally meaning "for (every) myriad (ten thousand)"
is accessible for free: true
license: CC-BY-NC-ND-2.5
software help: methodology.html

UniprotR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0078
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0637
application sub category: topic 3071
citation: J.JPROT.2019.103613
citation: pubmed:31843688
description: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase). Retrieving Information of Proteins from Uniprot. Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information. UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProtknowledgebase). M. Soudy, A. Anwar, E.A. Ahmed, et al., UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase), Journal of Proteomics (2019), https://doi.org/10.1016/j.jprot.2019.103613
feature list: operation_0337
feature list: operation 1812
feature list: operation 2422
license: GPL-3.0

Uniqprimer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0632
application sub category: topic 3168
application sub category: topic 3810
citation: PDIS-10-18-1819-RE
citation: pubmed:31436473
description: Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola | Uniqprimer, a software pipeline developed in Python, was deployed as a user-friendly internet tool in Rice Galaxy for comparative genome analyses to design primer sets for PCRassays capable of detecting target bacterial taxa. The pipeline was trialed with Dickeya dianthicola, a destructive broad-host-range bacterial pathogen found in most potato-growing regions. Dickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. Upon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with Uniqprimer, of which two were specific and sensitive when tested with D. dianthicola
feature list: operation_0308

UnityMol-APBS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0166
application sub category: topic_0176
application sub category: topic_0602
application sub category: topic_0821
citation: PRO.3773
citation: pmcid:PMC6933841
citation: pubmed:31710727
description: Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS. Implementation of a visualization prototype for molecular structures and networks using the Unity3D game engine. Implementation of numerous graphical methods as spheres, particle systems, bond, etc.
feature list: operation_0337
feature list: operation_0409
feature list: operation 2476
license: GPL-3.0

UniversalMer
type: SoftwareApplication
input: RNA sequence
  type: FormalParameter
  additional type: data 3495
  encoding format: format 2546
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 2546
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 2546
output: Base frequencies table
  type: FormalParameter
  additional type: data 1265
output: Base word frequencies table
  type: FormalParameter
  additional type: data 1266
output: Text
  type: FormalParameter
  additional type: data 3671
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0091
application sub category: topic 3473
description: UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists.
feature list: operation 3472
is accessible for free: true
license: Freeware
operating system: Mac
operating system: Windows
software version: 2.0.0

VADR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0160
application sub category: topic_0622
application sub category: topic_0623
application sub category: topic_0781
citation: s12859-020-3537-3
citation: pmcid:PMC7245624
citation: pubmed:32448124
description: Classification and annotation of viral sequences based on RefSeq annotation.
feature list: operation_0361
feature list: operation_0363
feature list: operation_0447
feature list: operation 3431

VAPPER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2830
application sub category: topic 3168
application sub category: topic 3308
citation: GIZ091
citation: pmcid:PMC6735694
citation: pubmed:31494667
description: High-throughput variant antigen profiling in African trypanosomes of livestock | Variant Antigen Profiling for Trypanosoma congolense and Trypanosoma vivax | Trypanosomes are important human and veterinary parasites that cause potentially lethal blood infections and a chronic wasting disease (African trypanosomiasis). These organisms use antigenic variation to evade the host immune response, for which their genomes contain many hundreds of variable antigen genes. Making sense of this hypervariable repertoire is a major challenge in genome analysis and a bottleneck in vaccine development | the VAPPER code for the first time, please type:
feature list: operation 2939
feature list: operation 3227
feature list: operation 3891

VARIDT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3295
application sub category: topic 3375
application sub category: topic 3577
citation: gkz779
citation: pmcid:PMC6943059
citation: pubmed:31495872
description: Search for Drug Transporter Entries: | Examples: P-glycoprotein 1 ; BCRP ; OATP1B1 ; Oxaliplatin ; Lung cancer .. | Search Drug Transporter by Transporter Name: | J. Y. Yin, W. Sun, F. C. Li, J. J. Hong, X. X. Li, Y. Zhou, Y. J. Lu, M. Z. Liu, X. Zhang, N. Chen, X. P. Jin, J. Xue, S. Zeng * , L. S. Yu * & F. Zhu * . VARIDT 1.0: Variability of Drug Transporter Database. Nucleic Acids Research . doi: 10.1093/nar/gkz779 (2020). PMID: 31495872
feature list: operation 2495
feature list: operation 3202

VARUS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3512
citation: S12859-019-3182-X
citation: pmcid:PMC6842140
citation: pubmed:31703556
description: sampling complementary RNA reads from the sequence read archive. VARUS: Drawing Diverse Samples from RNA-Seq Libraries. VARUS was originally written by Willy Bruhn as a Bachelors' thesis supervised by Mario Stanke. This repository is a copy of https://github.com/WillyBruhn/VARUS made in November 2018 and contains many bugfixes, an incremental intron database feature and an extension for using HISAT al alternative alignment program
feature list: operation_0362
feature list: operation_0524
feature list: operation 3258
feature list: operation 3431

VASE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0154
application sub category: topic 2814
application sub category: topic 2828
citation: PRO.3788
citation: pmcid:PMC6933850
citation: pubmed:31724231
description: VASE is a web-tool for visualizing alignments on a protein structure. It allows you to enter the ID of a protein structure in PDB format for which VASE will generate an interface. VASE will show a set of homologous sequences, aligned to the sequence of your structure, along with entropy/variability data and a 3D interface. Here's an example: 1CRN.
feature list: operation_0292
feature list: operation_0295
feature list: operation_0319
feature list: operation_0570
feature list: operation 2488

VASSL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3474
citation: TVCG.2019.2934266
citation: pubmed:31425086
description: A Visual Analytics Toolkit for Social Spambot Labeling | Visual Analytics Toolkit for Social Spambots Labeling | The server is currently busy. Please wait. | Thank you for your participation | You have completed all the sessions | Label as Spambot Label as Genuine | Please express your opinion about VASSL:
feature list: operation 3891

VCF-DART
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3676
citation: J.JMOLDX.2019.07.001
citation: pubmed:31442673
description: A Customizable Analysis Pipeline for Identification of Clinically Relevant Genetic Variants in Next-Generation Sequencing Data | In this article, we introduce the variant call format-diagnostic annotation and reporting tool (VCF-DART), a customized analysis pipeline tool for the rapid annotation of variants from exome or genome sequencing and the generation of reports for genetic diagnostics. VCF-DART uses custom gene lists to categorize variants into specific analysis tiers and to subcategorize them on the basis of standard parameters to facilitate the rapid interrogation of potentially pathogenic variants by human operators
feature list: operation 3225
feature list: operation 3227

VCF-Server
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3068
application sub category: topic 3168
application sub category: topic 3473
citation: MGG3.641
citation: pmcid:PMC6625089
citation: pubmed:31127704
description: A web-based visualization tool for high-throughput variant data mining and management.
feature list: operation 1812
feature list: operation 3227
feature list: operation 3675
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: VCF-Server-Manual-EN.pdf
primary contact: https://orcid.org/0000-0001-8347-0830

VCF2PopTree
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic 2885
citation: PEERJ.PREPRINTS.27682V2
description: a one-click client-side software to construct population phylogeny from genome-wide SNPs. VCF2PopTree is a client-side software written in Javascript and it runs. purely within the user’s computer/browser. VCF2PopTree is compatible
feature list: operation_0323
feature list: operation_0326
feature list: operation 3196
license: MIT

VCPA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0769
application sub category: topic 3673
application sub category: topic 3676
citation: bty894
citation: pmcid:PMC6513159
citation: pubmed:30351394
description: SNP/Indel Variant Calling Pipeline and data management tool used for analysis of whole genome and exome sequencing (WGS/WES) for the Alzheimer’s Disease Sequencing Project.
feature list: operation_0452
feature list: operation 3196
feature list: operation 3227
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
software help: doc

VDING
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3068
application sub category: topic 3452
citation: JOURNAL.PONE.0225823
citation: pmcid:PMC6890217
citation: pubmed:31794595
description: Use of three points to determine the accuracy of guided implantation.
feature list: operation_0337
feature list: operation 3435
license: GPL-3.0

VDJbase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic_0804
citation: gkz872
citation: pmcid:PMC6943044
citation: pubmed:31602484
description: an adaptive immune receptor genotype and haplotype database. The adaptive immune receptor Genotype and Haplotype database. 11-Oct-2019 *NEW* - VDJbase is described in Nucleic Acids Research. VDJbase is a publicly available database that offers easy searching of genotype and haplotype data inferred from AIRR-seq datasets. From these data we can explore the variability of the genomic loci of the Ig and TR encoding genes across populations
feature list: operation_0337
feature list: operation_0487
feature list: operation 2421
feature list: operation 3196

VDJdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0160
application sub category: topic_0219
application sub category: topic 2830
citation: GKZ874
citation: pubmed:31588507
description: VDJdb is a database extension, new analysis infrastructure and a T-cell receptor motif compendium.
feature list: operation_0224
feature list: operation_0238
feature list: operation_0416

VEF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2885
application sub category: topic 3474
application sub category: topic 3673
application sub category: topic 3676
citation: BTZ952
citation: pubmed:31873730
description: a Variant Filtering tool based on Ensemble methods. Variant Ensemble Filter, an ensemble based filter for VCF files. VEF is designed for filtering variants of single non-cancerous samples. This bash script calls example script vef_clf.py and vef_apl.py located in the example/ directory to train and apply the filter, respectively. After running test.sh, there will be 2 filter models in example/data with the .clf extension, along with 2 filtered VCF files with the .vef.vcf extension
feature list: operation 3227
feature list: operation 3359
feature list: operation 3675
feature list: operation 3695
license: MIT

VETA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3077
application sub category: topic 3304
application sub category: topic 3500
citation: FNINS.2019.00975
citation: pmcid:PMC6753167
citation: pubmed:31572120
description: An Open-Source Matlab-Based Toolbox for the Collection and Analysis of Electromyography Combined With Transcranial Magnetic Stimulation. The combination of electromyography (EMG) and transcranial magnetic stimulation (TMS) offers a powerful non-invasive approach for investigating corticospinal excitability in both humans and animals. Acquiring and analyzing the data produced with this combination of tools requires overcoming multiple technical hurdles. Due in part to these technical hurdles, the field lacks standard routines for EMG data collection and analysis. This poses a problem for study replication and direct comparisons. Although software toolboxes already exist that perform either online EMG data visualization or offline analysis, there currently are no openly available toolboxes that flexibly perform both and also interface directly with peripheral EMG and TMS equipment
feature list: operation_0337

VEnCode
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
author: https://orcid.org/0000-0001-6985-4520
description: Performs intersectional genetics-related operations to find VEnCodes using databases provided by the FANTOM5 consortium, namely the CAGE enhancer and transcription start site (TSS) databases. For more information on the VEnCode technology, please refer to Macedo and Gontijo, bioRxiv 2019
is accessible for free: true
license: BSD-3-Clause
software version: 0.1.0
primary contact: https://orcid.org/0000-0001-6985-4520

VGE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0769
application sub category: topic 3372
citation: S12859-019-3085-X
citation: pmcid:PMC6886159
citation: pubmed:31787090
description: Virtual Grid Engine (VGE) is a kind of middleware for running bioinformatics software pipelines on large-scale supercomputers which do not support any grid engine survices. VGE employs master-worker model. It first reserves processors and/or cores by running the job which is parallelized by MPI, then asign divided small tasks onto its worker processes. VGE is written in python.
feature list: operation 3359

Viral Host Range database
type: SoftwareApplication
output: Evidence
  type: FormalParameter
  additional type: data 2042
  encoding format: format 3620
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
additional type: Web application
application sub category: topic_0781
application sub category: topic 3489
author: https://orcid.org/0000-0002-7141-6340
author: Bryan Brancotte
citation: btab070
citation: pmcid:PMC8428608
citation: pubmed:33594411
contributor: https://orcid.org/0000-0002-7141-6340
description: The Viral Host Range database represents a unique resource for the community to rapidly find, document analyze and disseminate data related to the range of hosts that a virus can infect. Over the years, countless host range experiments have been performed in many laboratories. However, these data are not readily available to the community and are therefore underexploited. The VHRdb is an online resource that centralizes experimental data related to the host range of viruses. While it originates from bacteriophages and bacteria interaction studies, its design is compatible with viruses infecting all living forms. Users can browse publicly available data to find which host is infected by a virus, and vice versa. Users can also upload their own data while keeping it private or making it public, analyze results across independent sets of data, generate and visualize outputs. Data implemented in the VHRdb are linked to users and, if available, to publications and sequence identifiers.
feature list: operation 3436
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: viralhostrangedb
software version: 1
primary contact: https://orcid.org/0000-0001-6875-5758

VIBRANT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0602
application sub category: topic 3174
application sub category: topic 3407
application sub category: topic 3697
citation: https://doi.org/10.1101/855387
citation: v1
description: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. Virus Identification By iteRative ANnoTation. Discovery Environment Applications List. Created by upendra_35, last modified on Nov 04, 2019. If you find VIBRANT useful please consider citing our preprint on bioRxiv:. Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387. VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies. The QuickStart tutorial provides an introduction to basic DE functionality and navigation. Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions
feature list: operation_0362
feature list: operation 3192
feature list: operation 3216
license: GPL-3.0

VIC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3400
citation: S13073-019-0664-4
citation: pmcid:PMC6708137
citation: pubmed:31443733
description: a computational tool for assessing clinical impacts of somatic variants | A Computational Tool for Assessing Clinical Impacts of Somatic Variants Following the AMP-ASCO-CAP 2017 Guidelines | Variant Interpretation for Cancer (VIC) | Clinical Interpretations of Variants in Cancer | java -jar target/VIC-1.0-jar-with-dependencies.jar [-b ] [-d ] [-h] [-input_type ] [-i ] [-cancer_type ] [-convert2annovar ] [-l ] [-skip_annovar] [-o ] [-annotate_variation ] [-table_annovar ] [-s ] [-otherinfo ] [-db ]
feature list: operation 1812
feature list: operation 3225
feature list: operation 3227

VICTOR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 2830
application sub category: topic 3421
citation: https://doi.org/10.1101/756809
description: A precision virtual crossmatch decision support system for interpretation of ambiguous molecular HLA typing data | VICTOR: VIrtual CrossmaTch for mOleculaR typing data | This prototype tool computes virtual crossmatch using the candidate’s unacceptable antigens including high resolution alleles and molecular HLA typing of the donor | Web services interface information for Transplanttoolbox
feature list: operation_0416
feature list: operation 3196
feature list: operation 3891

VIO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic 3308
application sub category: topic 3379
application sub category: topic 3400
citation: S12859-019-3194-6
citation: pmcid:PMC6927110
citation: pubmed:31865910
description: ontology classification and study of vaccine responses given various experimental and analytical conditions. VIO: Vaccine Investigation Ontology. Statistics of Vaccine Investigation Ontology. IRI: https://raw.githubusercontent.com/vaccineontology/VIO/master/src/ontology/vio.owl. VIO and its usage in studying Yellow Fever vaccine-induced host response were presented in the VDOS-2018 workshop: https://sites.google.com/site/vdosworkshop/VDOS-2018. Note: This version of statistics metrics does not include any instance data yet. This feature will be added in the future
feature list: operation_0560
feature list: operation 3431
feature list: operation 3435
feature list: operation 3501

VIPER LC-MS
type: SoftwareApplication
input: Mass spectrometry spectra
  type: FormalParameter
  additional type: data_0943
  encoding format: format 3654
  encoding format: format 3834
input: Peptide mass fingerprint
  type: FormalParameter
  additional type: data_0944
  encoding format: format 3752
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic 3382
application sub category: topic 3520
citation: pubmed:17545182
description: VIPER is primarily intended for processing deisotoped data from high mass measurement accuracy instruments (e.g. FT, TOF, or Orbitrap) and comparing the features found to a list of expected peptides (aka mass and time (MT) tags), as practiced by the AMT tag approach. The software allows one to display the data as a two-dimensional plot of spectrum number (i.e. elution time) vs. mass. It can read MS data from several file formats: .PEK, .CSV (Decon2LS format), .mzXML, and .mzData.
feature list: operation 3203
feature list: operation 3432
feature list: operation 3627
feature list: operation 3628
feature list: operation 3694
feature list: operation 3695
license: Apache-2.0

VISDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0622
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 2640
application sub category: topic 3512
citation: gkz867
citation: pmcid:PMC6943068
citation: pubmed:31598702
description: a manually curated database of viral integration sites in the human genome. VISDB, visdb, virus integration site, viral integration, DNA virus, retrovirus, HBV, HPV, HIV, HTLV-1, EBV, AAV2, MCV, MLV, XMRV, gene, fragile site, miRNA, database, resource, UTHealth, SBMI, Zhongming Zhao
feature list: operation_0238
feature list: operation_0440
feature list: operation_0463

VISION
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3168
application sub category: topic 3173
citation: https://doi.org/10.1101/730358
description: Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of mouse hematopoietic cells | ValIdated Systematic IntegratiON of hematopoietic epigenomes | The VISION project aims to harvest truly valuable information from the flood of epigenomic data on hematopoietic cells as
feature list: operation_0441
feature list: operation 3557

VISOR
type: SoftwareApplication
input: Sequence features metadata
  type: FormalParameter
  additional type: data 2914
  encoding format: format 3003
input: DNA sequence
  type: FormalParameter
  additional type: data 3494
  encoding format: format 1929
output: Sequence variations
  type: FormalParameter
  additional type: data 3498
  encoding format: format 2331
output: Sequence variations
  type: FormalParameter
  additional type: data 3498
  encoding format: format 2572
output: Sequence variations
  type: FormalParameter
  additional type: data 3498
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic 3175
application sub category: topic 3511
author: https://orcid.org/0000-0002-8735-8093
citation: BTZ719
citation: pubmed:31589307
description: Haplotype-aware structural variants simulator for short, long and linked reads
feature list: operation 2426
feature list: operation 2928
feature list: operation 3208
is accessible for free: true
license: LGPL-3.0
software help: visordoc
software version: 1.0

VIST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2640
application sub category: topic 3379
application sub category: topic 3577
citation: S12859-019-2958-3
citation: pmcid:PMC6697931
citation: pubmed:31419935
description: a Variant-Information Search Tool for precision oncology | The Variant Information Search Tool developed @ WBI
feature list: operation 2421
feature list: operation 3280

VMD Store
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3382
application sub category: topic 3489
application sub category: topic 3892
citation: ACS.JCIM.9B00739
citation: pubmed:31682440
description: VMD Plugin to Browse, Discover, and Install VMD Extensions. In this page, you can find all the possible alternatives to install the VMD Store extension. 1. Install VMD Store through VMD Tk Console This installation process can be used ... Biomolecular SIMulations Research Group
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VMH
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conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0602
application sub category: topic 3407
application sub category: topic 3697
citation: gky992
citation: pmcid:PMC6323901
citation: pubmed:30371894
description: Virtual Metabolic Human (VMH) database captures information on human and gut microbial metabolism and links this information to hundreds of diseases and nutritional data.
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is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: https://orcid.org/0000-0002-8071-7110

VNA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3416
application sub category: topic 3452
citation: jor.24568
citation: pmcid:PMC7790441
citation: pubmed:31840849
description: Vascular Network Analysis (VNA) is a novel analysis protocol based on freely available or commonly used software to generate vascular data from μCT scans.
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license: GPL-3.0

VOCCluster
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application sub category: topic 3172
application sub category: topic 3407
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citation: ACS.ANALCHEM.9B03084
citation: pubmed:31791122
description: Untargeted Metabolomics Feature Clustering Approach for Clinical Breath Gas Chromatography. Metabolic profiling of breath analysis involves processing, alignment, scaling and clustering of thousands of features ex-tracted from Gas Chromatography Mass spectrometry (GC-MS) data from hundreds of participants. The multi-step data processing is complicated, operator error-prone and time-consuming. Automated algorithmic clustering methods that are able to cluster features in a fast and reliable way are necessary. These accelerate metabolic profiling and discovery plat-forms for next generation medical diagnostic tools. Our unsupervised clustering technique, VOCCluster, prototyped in Py-thon, handles features of deconvolved GC-MS breath data. VOCCluster was created from a heuristic ontology based on the observation of experts undertaking data processing with a suite of software packages.
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VOLARE
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application sub category: topic 3697
citation: S12859-019-3021-0
citation: pmcid:PMC6701114
citation: pubmed:31429723
description: visual analysis of disease-associated microbiome-immune system interplay | Visualization of Linear Regression Elements | Visualization of linear regression elements comparing microbiome and immune system readouts
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VOLPES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0154
citation: GKZ407
citation: pmcid:PMC6602475
citation: pubmed:31114895
description: VOLPES (Visualization Of PhysicochEmical Sequence properties) - interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences.
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is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation.html
software help: tutorial.html
primary contact: https://orcid.org/0000-0003-3814-3675

VPAC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic 3170
application sub category: topic 3308
citation: S12859-019-2742-4
citation: pmcid:PMC6509870
citation: pubmed:31074382
description: Variational projection for accurate clustering of single-cell transcriptomic data.
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feature list: operation 3891
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Rui Jiang

VPOT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0622
application sub category: topic 3168
citation: j.gpb.2019.11.001
citation: pmcid:PMC7056850
citation: pubmed:31765830
description: A Customizable Variant Prioritization Ordering Tool for Annotated Variants. VPOT - Variant Prioritisation Ordering Tool. VPOT is a Python tool written to allow prioritisation of variants in ANNOVAR annotated VCF files. VPOT is a Python tool written to allow prioritisation of variants in ANNOVAR annotated VCF files. VPOT provides various functions for the purpose of speeding up variant discovery
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license: GPL-3.0

VRTK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 2258
application sub category: topic 3292
application sub category: topic 3315
application sub category: topic 3332
citation: CHEMRXIV.6629150.V2
description: Exploring Drugbank in Virtual Reality Chemical Space. VRTK is a toolkit to rapidly build VR solutions. VRTK is a collection of useful, reusable solutions to common problems found when building for virtual reality. VRTK aims to help productivity by speeding up the creation process from prototyping ideas to building complete solutions
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VTA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0611
application sub category: topic 3170
citation: ejn.14534
citation: pmcid:PMC6972656
citation: pubmed:31374129
description: Transcriptional profiling aligned with in situ expression image analysis reveals mosaically-expressed molecular markers for GABA neuron sub-groups in the ventral tegmental area | VTA Expression Data Extractor
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VaDER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
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application sub category: topic 3334
application sub category: topic 3384
application sub category: topic 3399
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citation: GIZ134
citation: pmcid:PMC6857688
citation: pubmed:31730697
description: Deep learning for clustering of multivariate clinical patient trajectories with missing values. Deep learning for clustering of multivariate short time series with potentially many missing values. This repository contains code for a new method for clustering multivariate short time series with potentially many missing values (published here), a setting commonly encountered in the analysis of longitudinal clinical data, but generally still poorly addressed in the literature. Supporting code for the manuscript "Deep learning for clustering of multivariate clinical patient trajectories with missing values". Supporting code for the manuscript "Deep learning for clustering of multivariate clinical patient trajectories with missing values"
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license: LGPL-2.1

VarCover
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3053
application sub category: topic 3277
citation: J.JMOLDX.2019.10.005
citation: pubmed:31751680
description: Allele Min-Set Cover Software. To facilitate reference-material selection for clinical genetic testing laboratories, we developed VarCover, open-source software hosted on GitHub, which accepts a file of variants (rsIDs or VCF) and returns an approximately minimal set of samples covering the targeted alleles. VarCover employs the SetCoverPy package, sample weights, and preselection of singleton-possessing samples to efficiently solve the min-set cover problem. As a test case, we attempted to find a minimal set of reference samples from the 1000 Genomes Project to cover 237 variants considered putatively pathogenic (of which 12 were classified as pathogenic or likely pathogenic) in the original 56 medically actionable genes recommended by the American College of Medical Genetics and Genomics (ACMG). The number of samples, number of alleles, and processing time were measured in subsets of the 237 target alleles.

VarFish
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3325
description: VarFish is an easy-to-use web-based database system designed for empowering geneticists in the analysis of clinical and whole exome sequencing variant data sets for individuals and families. It provides a set of tools for supporting the full workflow from (i) variant data quality control, (ii) variant filtration and (iii) efficient assessment of variants based on visual alignment inspection and annotation data such as functional and frequency annotation.
license: MIT

VarGen
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
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application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 2885
application sub category: topic 3517
citation: BTZ930
citation: pubmed:31834354
description: VarGen is an R package designed to get a list of variants related to a disease. It just need an OMIM morbid ID as input and optionally a list of tissues / gwas traits of interest to complete the results. You can also use your own customised list of genes. VarGen is capable of annotating the variants to help you identify the most impactful ones.
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license: MIT

VarGenius
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2533
citation: s12859-018-2532-4
citation: pmcid:PMC6291943
citation: pubmed:30541431
description: VarGenius is a platform for analysis of variants from DNA sequencing data. Currently it can be used for WES and Panels. Starting from fastq files it can execute the GATK Best Practices pipeline doing both single calling and joint calling. Then it executes Annovar for variant annotation and generates a readable output in tabular and XLS format. All the data extracted from the samples (variants, genotypes, etc..) are uploaded into a Postgres database which can be used for further downstream analyses.
is accessible for free: true
operating system: Linux
software help: GUIDE
software version: 1.0
primary contact: https://orcid.org/0000-0001-9440-1080

VarMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0166
application sub category: topic_0654
citation: btz482
citation: pmcid:PMC6853667
citation: pubmed:31192369
description: Tool for mapping a list of chromosome coordinates, and their variants, to the corresponding protein residues in the canonical UniProt protein sequence.
feature list: operation_0321
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is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/DisaStr/GetPage.pl
primary contact: James Stephenson

VarSelLCM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
citation: bty786
citation: pubmed:30192923
description: Package for variable selection in model-based clustering of mixed-data with missing values.
feature list: operation 3432
feature list: operation 3557
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: varsellcm.r-forge.r-project.org
software help: VarSelLCM.pdf
software version: 2.1.3
primary contact: Mohammed Sedki

VarSight
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
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application sub category: topic_0625
application sub category: topic 3325
application sub category: topic 3577
application sub category: topic 3676
citation: S12859-019-3026-8
citation: pmcid:PMC6792253
citation: pubmed:31615419
description: prioritizing clinically reported variants with binary classification algorithms. VarSight is a collection of scripts used to test the application of classification algorithms for identifying variants that will be returned on a clinical report. VarSight relies on Codicem to perform common clinical pipeline pre-processing, namely variant annotation and filtering. In addition to data available in Codicem, it also uses gene rankings that are based on Human Phenotype Ontology (HPO) terms using both a built in calculation (cosine score) and the external tool PyxisMap. The classifiers in VarSight ingest a total of 95 features that are run through a feature selection process to get the top 20 features. Those 20 features are used to test both classification of reported variants and prioritization of reported variants in a larger filtered list. Results from the latest version of VarSight tests are available in the folder labeled "paper"
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VarSite
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conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
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application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 2814
application sub category: topic 3120
citation: PRO.3746
citation: pmcid:PMC6933866
citation: pubmed:31606900
description: Disease variants and protein structure. Disease Variants and Structure
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Vargas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic 3169
application sub category: topic 3170
citation: https://doi.org/10.1101/2019.12.20.884676
description: heuristic-free alignment for assessing linear and graph read aligners. Vargas computes optimal alignments of short reads to a directed acyclic graph (DAG). After building a graph, reads are aligned using a SIMD-vectorized version of the Smith-Waterman dynamic programming algorithm, with 16 -- 64 reads per vector depending on the instruction set
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license: MIT

VariBench
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0128
application sub category: topic 2885
application sub category: topic 3320
citation: https://doi.org/10.1101/634766
description: Benchmark database suite comprising variation datasets for testing and training methods for variation effect prediction.
feature list: operation_0331
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is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows

VariCarta
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0219
application sub category: topic 3068
application sub category: topic 3168
application sub category: topic 3298
citation: AUR.2236
citation: pubmed:31705629
description: A Comprehensive Database of Harmonized Genomic Variants Found in Autism Spectrum Disorder Sequencing Studies. VariCarta is a curated, web-based database housing ASD-linked genes created from the meta-analysis of -omic sequencing literature. VariCarta is a database of human DNA genetic variants found in individuals diagnosed with Autism Spectrum Disorder (ASD) and reported in peer-reviewed scientific literature.
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VariMerge
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic 3174
citation: BTZ350
citation: pmcid:PMC6612864
citation: pubmed:31510647
description: Building large updatable colored de Bruijn graphs via merging | VARI-merge is a pair of tools (vari-merge and color-merge) capable of merging the succinct colored de Bruijn graphs produced by VARI. The VARI-merge branch includes all of VARI | Cosmo is a fast, low-memory DNA assembler that uses a succinct de Bruijn graph | VARI is an extension to Cosmo and supports offline construction of succinct colored de Bruijn graphs. It can be found in the VARi branch, however all the components are also in this branch. You should use this branch for the VARI tools because it includes an important bugfix: Palendromes are not duplicated during the revcomp generation phase of succinct de Bruijn graph construction
feature list: operation_0524
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feature list: operation 3472
license: GPL-3.0

VariantStore
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0634
application sub category: topic 3577
citation: https://doi.org/10.1101/2019.12.24.888297
description: A Large-Scale Genomic Variant Search Index.
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feature list: operation 2422
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feature list: operation 3227

VariantValidator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0203
citation: humu.23348
citation: pmcid:PMC5765404
citation: pubmed:28967166
description: VariantValidator is a user-friendly software tool designed to validate the syntax and parameters of DNA variant descriptions according to the HGVS Sequence Variant Nomenclature. VariantValidator ensures that users are guided through the intricacies of the HGVS nomenclature, e.g. if the user makes a mistake, VariantValidator automatically corrects the mistake if it can, or provides helpful guidance if it cannot. In addition, VariantValidator accurately inter-converts between transcript variant descriptions and genomic variant descriptions in HGVS and Variant Call Format (VCF) VariantValidator interfaces with the hgvs package to parse, format, and manipulate biological sequence variants. See https://github.com/biocommons/hgvs/ for details of the hgvs package VariantValidator is a highly functional platform enabling high-throughput and embeddable utilisation of functionality of https://variantvalidator.org/
feature list: operation 1812
feature list: operation 3227
license: AGPL-3.0

Variant Combination Pathogenicity Predictor (VarCoPP) 2.0
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic_0199
application sub category: topic_0622
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application sub category: topic_0634
application sub category: topic 3063
application sub category: topic 3325
author: Sofia Papadomitriou
citation: pnas.1815601116
citation: s12859-023-05291-3
citation: pmcid:PMC10152795
citation: pmcid:PMC6575632
citation: pubmed:31127050
citation: pubmed:37127601
description: VarCoPP is a machine learning method that predicts the potential pathogenicity of variant combinations in gene pairs. It is based on digenic data present in OLIDA and it was trained against variants from the 1000 Genomes Project. VarCoPP2.0 is a Balanced Random Forest predictor consisting of 400 decision trees. A variant combination can be either predicted as disease-causing (i.e. candidate or probably pathogenic) or neutral (i.e. probably neutral). VarCoPP can be applied for Single Nucleotide Variants (SNVs) and small insertions/deletions from a single individual. It is highly recommended to perform beforehand an initial variant filtering procedure and generally restrict the analysis to variants from up to 150 genes. VarCoPP was developed in the Interuniversity Institute of Bioinformatics in Brussels, under the collaboration of Université libre de Bruxelles and Vrije Universiteit Brussel. You can use it through the online tool ORVAL: https://orval.ibsquare.be.
feature list: operation 2423
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is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: Interuniversity Institute of Bioinformatics in Brussels
software version: 1.0
software version: 2.0
primary contact: https://orcid.org/0000-0003-3645-1455

Variant Score Ranker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3676
citation: BTZ252
citation: pubmed:31086968
description: Variant Score Ranker (VSR) - web application for intuitive missense variant prioritization.
feature list: operation_0331
feature list: operation 3225
feature list: operation 3226
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: tab-9158-3
software help: tab-9158-4
primary contact: Dennis Lal

Variational Bayes approach (GEMINI)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 3053
citation: s13059-019-1745-9
citation: pmcid:PMC6624979
citation: pubmed:31300006
description: Variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens.
feature list: operation_0487
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software help: gemini-quickstart.Rmd

Varstation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3053
application sub category: topic 3168
application sub category: topic 3303
citation: https://doi.org/10.1101/833582
description: a complete and efficient tool to support NGS data analysis. High precision on genetic analysis
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VegMarks
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 2885
application sub category: topic 3489
citation: JSBBS.18202
citation: pmcid:PMC6776151
citation: pubmed:31598083
description: Construction of a core collection of eggplant (Solanum melongena L.) based on genome-wide SNP and SSR genotypes. a DNA marker database for vegetables
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feature list: operation 3432

Venn-diaNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic 3170
application sub category: topic 3308
citation: S12859-019-3302-7
citation: pmcid:PMC6941187
citation: pubmed:31881980
description: venn diagram based network propagation analysis framework for comparing multiple biological experiments. Benjamin Hur, Dongwon Kang, Sangseon Lee, Ji Hwan Moon, Gung Lee and Sun Kim. Handles I/O between front-end & back-end. Currently, Venn-diaNet uses String DB
feature list: operation 2495
feature list: operation 2497
feature list: operation 3501

VeriNA3d
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0082
application sub category: topic_0097
application sub category: topic_0099
citation: btz553
citation: pubmed:31286135
description: R package for the analysis of nucleic acids structural data, with an emphasis in complex RNA structures.
feature list: operation_0279
feature list: operation 2518
feature list: operation 3095
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: documentation
primary contact: Modesto Orozco
primary contact: Pablo D. Dans

ViSEAGO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic_0659
citation: S13040-019-0204-1
citation: pmcid:PMC6685253
citation: pubmed:31406507
description: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity | The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study
feature list: operation 2942
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feature list: operation 3501
license: GPL-3.0

ViSiElse
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0092
citation: PEERJ.PREPRINTS.27665V2
description: An innovative visualization R package to ensure behavioral raw data reliability and transparency. Background In recent years, the scientific community encouraged the use of raw data graphs to improve the reliability and transparency of the results presented in papers. However, methods to visualize raw data are limited to one variable per graph and or only small samples. In behavioral science as in many other fields, multiple variables need to be plotted together to allow insights of the behavior or the process observations. In this paper, we present ViSiElse, an R-package offering a new approach in raw data visualization. Methods. ViSiElse was developed with the open-source software R to provide a solution for the complete visualization of the raw time data. Results. ViSiElse grants a global overview of a process by combining the visualization of multiple actions timestamps for all participants in a single graph. Individuals and or group behavior can easily be assessed
feature list: operation_0337
feature list: operation 3436

ViVa
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic_0780
citation: PLD3.147
citation: pmcid:PMC6658840
citation: pubmed:31372596
description: Accelerating structure-function mapping using the ViVa webtool to mine natural variation | If Autoforward does not work, follow this link to go to Clay's ViVa website..
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VICTOR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
description: VICTOR is an interactive and dependency-free visual analytics web application which allows the comparison and visualization of various clustering outputs.
feature list: operation_0337
feature list: operation 3432

VieClus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0108
application sub category: topic_0128
application sub category: topic 3474
citation: 978-1-4939-9873-9 16
citation: pubmed:31583641
description: Vienna Graph Clustering. The graph clustering framework VieClus -- Vienna Graph Clustering. The main project page of to open source framework VieClus -- Vienna Graph Clustering. This is the release of our memetic algorithm, VieClus (Vienna Graph Clustering), to tackle the graph clustering problem. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. In our experimental evaluation, we show that our algorithm successfully improves or reproduces all entries of the 10th DIMACS implementation challenge under consideration in a small amount of time. In fact, for most of the small instances, we can improve the old benchmark result in less than a minute. Moreover, while the previous best result for different instances has been computed by a variety of solvers, our algorithm can now be used as a single tool to compute the result. VieClus - Vienna Graph Clustering is a memetic algorithm
feature list: operation_0337
feature list: operation 3432
software help: vieclusv1.00.pdf

VikNGS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0625
application sub category: topic 3168
citation: btz716
citation: pmcid:PMC7703770
citation: pubmed:31580400
description: A C ++ Variant Integration Kit for Next Generation Sequencing Association Analysis. Documentation for VikNGS — VikNGS 0.0.1 documentation. Free document hosting provided by Read the Docs
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feature list: operation 3436
feature list: operation 3791

VirBin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
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application sub category: topic_0199
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic 3168
citation: S12859-019-3138-1
citation: pmcid:PMC6829986
citation: pubmed:31684876
description: The method is essentially an EM algorithm.
feature list: operation_0487
feature list: operation 3216
feature list: operation 3432
feature list: operation 3798

ViralPlaque
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic 3382
application sub category: topic 3474
citation: PEERJ.7729
citation: pmcid:PMC6764358
citation: pubmed:31579606
description: a Fiji macro for automated assessment of viral plaque statistics. Plaque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user's needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed
feature list: operation 3443
feature list: operation 3799

Vireo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3170
application sub category: topic 3308
citation: S13059-019-1865-2
citation: pmcid:PMC6909514
citation: pubmed:31836005
description: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.
feature list: operation 3196
feature list: operation 3200
feature list: operation 3226
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: vireosnp.readthedocs.io

VirtualCytometry
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 2229
citation: btz610
citation: pmcid:PMC9883706
citation: pubmed:31373613
description: > HOMEPAGE MISSING! | a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data | MOTIVATION:The immune system has diverse types of cells that are differentiated or activated via various signaling pathways and transcriptional regulation upon challenging conditions. Immunophenotyping by flow and mass cytometry are the major approaches for identifying key signaling molecules and transcription factors directing the transition between the functional states of immune cells. However, few proteins can be evaluated by flow cytometry in a single experiment, preventing researchers from obtaining a comprehensive picture of the molecular programs involved in immune cell differentiation. Recent advances in single-cell RNA sequencing (scRNA-seq) have enabled unbiased genome-wide quantification of gene expression in individual cells on a large scale, providing a new and versatile analytical pipeline for studying immune cell differentiation
feature list: operation 2495

VisFeature
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: BTZ689
citation: pubmed:31504195
description: a stand-alone program for visualizing and analyzing statistical features of biological sequences | For Microsoft Windows platform, just download the VisFeature-win32-x64.zip package from https://github.com/wangjun1996/VisFeature/releases. Unpack it to your favorite location and then open VisFeature.exe | We have tested these codes on Windows10-64bit platform and Ubuntu 16.04.5 LTS platform. There is no guarantee that these codes can be compiled and executed on other platforms without modifications
feature list: operation 2422
license: GPL-3.0

VisR
type: SoftwareApplication
input: Alignment
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  additional type: data 1916
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  encoding format: format 3751
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0092
citation: 1471-2105-16-s11-s2
citation: pmcid:PMC4559603
citation: pubmed:26328469
description: A framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise.
feature list: operation_0337
feature list: operation 2409
feature list: operation 3680
is accessible for free: true
license: LGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: guide
software version: 0.9.4

VisioProt-MS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic 2830
application sub category: topic 3520
citation: https://doi.org/10.1177/1177932219868223
citation: pmcid:PMC6698994
citation: pubmed:31452600
description: Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS | Single test file Multiple test files | If you use VisioProt-MS for your research please cite: | Marie Locard-Paulet, Julien Parra, Renaud Albigot, Emmanuelle Mouton-Barbosa, Laurent Bardi, Odile Burlet-Schiltz, Julien Marcoux; VisioProt-MS: interactive 2D maps from intact protein mass spectrometry, Bioinformatics, bty680, https://doi.org/10.1093/bioinformatics/bty680 | You are in test mode. Click on a button to select a single test file or multiple test files. Uncheck to exit and upload your own data
feature list: operation 3629
feature list: operation 3633

VizGVar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3512
citation: btx694
citation: pubmed:29091996
description: Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains.
feature list: operation 3202
feature list: operation 3798
software help: doc
software version: 1.5
primary contact: Allan Orozco-Solano
primary contact: Antonio Solano-Román

WASPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0078
application sub category: topic_0102
application sub category: topic_0798
citation: btz745
citation: pmcid:PMC7703779
citation: pubmed:31589313
description: Web-Assisted Symbolic Plasmid Synteny Server.
feature list: operation_0578
feature list: operation 2421

WATCLUST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0166
application sub category: topic_0176
application sub category: topic 2275
citation: btv411
citation: pubmed:26198103
description: Tool for improving the design of drugs based on protein-water interactions.
feature list: operation_0482
feature list: operation 2415
feature list: operation 2476
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: examples
software help: using-watclust
primary contact: Adrian G. Turjanski
primary contact: Marcelo A. Marti

WAVES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
additional type: Web API
additional type: Web application
additional type: Web service
application sub category: topic_0091
application sub category: topic 3372
author: Marc Chakiachvili
citation: bty639
citation: pubmed:30052762
description: WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications. In order to fulfill the service’s computational needs, WAVES can perform computation on various resources and environments, such as Galaxy instances.
feature list: operation 3763
is accessible for free: true
license: GPL-3.0
operating system: Linux
provider: LIRMM
software help: waves-core.readthedocs.io
software help: installation.html
software version: 1.6
primary contact: Vincent Lefort

An Efficient Technique for White Blood Cells Nuclei Automatic Segmentation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2229
application sub category: topic 3344
application sub category: topic 3382
description: This code is implementation of an algorithm to segment the nucleus of white blood cells (WBCs)
feature list: operation 3443
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.1.0.0
primary contact: Mostafa M. A. Mohamed

WBNPMD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 2640
citation: S12967-019-2063-4
citation: pmcid:PMC6757419
citation: pubmed:31547811
description: weighted bipartite network projection for microRNA-disease association prediction | BACKGROUND:Recently, numerous biological experiments have indicated that microRNAs (miRNAs) play critical roles in exploring the pathogenesis of various human diseases. Since traditional experimental methods for miRNA-disease associations detection are costly and time-consuming, it becomes urgent to design efficient and robust computational techniques for identifying undiscovered interactions. METHODS:In this paper, we proposed a computation framework named weighted bipartite network projection for miRNA-disease association prediction (WBNPMD). In this method, transfer weights were constructed by combining the known miRNA and disease similarities, and the initial information was properly configured. Then the two-step bipartite network algorithm was implemented to infer potential miRNA-disease associations
feature list: operation_0463
feature list: operation 3792

WENGAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic 2815
application sub category: topic 3673
citation: https://doi.org/10.1101/840447
description: Wengan is a new genome assembler that unlike most of the current long-reads assemblers avoids entirely the all-vs-all read comparison.
feature list: operation_0523
feature list: operation_0524
feature list: operation_0525
feature list: operation 3216
feature list: operation 3644
license: AGPL-3.0

WGDdetector
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic 3170
application sub category: topic 3308
citation: s12859-019-2670-3
citation: pmcid:PMC6375192
citation: pubmed:30760221
description: Pipeline for detecting whole genome duplication events using the genome or transcriptome annotations.
feature list: operation 3258
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Yongzhi Yang

WHISCY
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
application sub category: topic 3534
author: http://orcid.org/0000-0001-7369-1322
citation: prot.20842
citation: pubmed:16450362
description: WHISCY is a program to predict protein-protein interfaces. It is primarily based on conservation, but it also takes into account structural information. A sequence alignment is used to calculate a prediction score for each surface residue of your protein.
operating system: Linux
operating system: Mac
operating system: Windows
provider: http://orcid.org/0000-0001-7369-1322
software help: whiscy
software version: 1.0
primary contact: http://orcid.org/0000-0001-7369-1322

WHdenovo
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic 3168
citation: btz942
citation: pmcid:PMC7759745
citation: pubmed:31860070
description: A haplotype-aware de novo assembly of related individuals using pedigree sequence graph. A cost-effective approach to diploid assembly for single samples and trios. It includes the following steps: construct sequence graph from illumina, align long reads to the graph and partition these long reads to two haplotypes.
feature list: operation_0524
feature list: operation_0525
feature list: operation 3454
feature list: operation 3644
license: MIT

WIT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0102
application sub category: topic 3168
application sub category: topic 3810
citation: S0219720019500082
citation: pubmed:31057068
description: Fast and Memory Efficient Approach for Mapping NGS Reads to a Reference Genome.
feature list: operation 3198
feature list: operation 3211
is accessible for free: true
license: Unlicense
operating system: Linux
software help: read me.html
primary contact: Sanjeev Kumar

WITOD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0637
application sub category: topic_0659
application sub category: topic 3050
application sub category: topic 3697
citation: https://doi.org/10.1101/813444
description: A Tool for Within-Taxon Operational Taxonomic Unit Diversity Analysis. A Tool for Within-Taxon Operational Taxonomic Unit (OTU) Diversity. Please copy the OTU Table and the rep_set.fna file into the same directory of witod.py and util directory
feature list: operation 3192
feature list: operation 3196
feature list: operation 3798
license: GPL-3.0

WPD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3399
citation: https://doi.org/10.15172/PNEU.2013.2/245
citation: pmcid:PMC6707408
citation: pubmed:31463184
description: a multi-dimensional program organised around World Pneumonia Day | There are limited examples of population-based approaches that engage a broad range of stakeholders for prevention of pneumonia. In 2010, a multi-dimensional public-private partnership was established around World Pneumonia Day (WPD) in Seoul, Korea and included the following components: a) formation of an expert advisory group, b) creation of educational materials tailored for lay persons, c) creation of a dedicated WPD internet website in the local language, d) organisation of a WPD venue in central Seoul, e) creation of video and social networking messages for wide distribution, and f) engagement of parents, health-care professionals, public health agencies and policymakers

WPMIAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3512
citation: BTZ820
citation: pubmed:31693067
description: Whole-degradome-based Plant MicroRNA-Target Interaction Analysis Server. If you use WPMIAS, please cite this article: Yuhan Fei, Yiyang Mao, Chengji Shen, Rui Wang, Hongsheng Zhang, Ji Huang, "WPMIAS: Whole-degradome-based Plant MicroRNA-Target Interaction Analysis Server", Bioinformatics, 2019, in press. DOI:10.1093/bioinformatics/btz820
feature list: operation_0463
feature list: operation 3454
feature list: operation 3792

WPTherml
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic 3314
application sub category: topic 3315
citation: CHEMRXIV.8341046.V2
description: A Python Package for the Design of Materials for Harnessing Heat. Pioneering the design of materials to harness heat. WPTherml stands for William Paterson University's tool for Thermal Energy and Radiation management with Multi Layer nanostructures. Project maintained by FoleyLab Hosted on GitHub Pages — Theme by mattgraham. WPTherml stands for William Paterson University’s tool for Thermal Energy and Radiation management with Multi Layer nanostructures.
feature list: operation_0337
feature list: operation 1812
feature list: operation 3435
license: GPL-3.0

Wang-xiaoheng
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0154
application sub category: topic_0736
citation: S12859-019-3276-5
citation: pmcid:PMC6929547
citation: pubmed:31874617
description: Prediction of protein structural classes by different feature expressions based on 2-D wavelet denoising and fusion. 2D-wavelet-for-protein-structural-classes-prediction We constructed a prediction model based on wavelet denoising using different feature expression methods. A new fusion idea, first fuse and then denoise, is proposed in this article. Two types of pseudo amino acid compositions are utilized to distill feature vectors. Then, a two-dimensional (2-D) wavelet denoising algorithm is used to remove the redundant information from two extracted feature vectors. The two feature vectors based on parallel 2-D wavelet denoising are fused, which is known as PWD-FU-PseAAC. The project includes three original datasets, source code for two-dimensional wavelet denoising and source code for feature vector prediction
feature list: operation_0267
feature list: operation_0303
feature list: operation_0474

Wannier90
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0605
application sub category: topic 3314
application sub category: topic 3372
citation: AB51FF
citation: pubmed:31658458
description: Wannier90 is a tool for obtaining maximally localized wannier functions from DFT calculations.
feature list: operation_0337

Warp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3077
application sub category: topic 3306
application sub category: topic 3316
application sub category: topic 3382
citation: S41592-019-0580-Y
citation: pmcid:PMC6858868
citation: pubmed:31591575
description: Real-time cryo-electron microscopy data preprocessing with Warp. If you just want to use Warp, all tutorials and binaries can be found at http://www.warpem.com. Continue reading this README only if you're interested in compiling Warp from source
feature list: operation_0337
feature list: operation 3431
feature list: operation 3458
license: GPL-3.0

WebAnno
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0218
application sub category: topic_0621
application sub category: topic 3474
citation: bbz130
citation: pmcid:PMC7820865
citation: pubmed:31838514
description: WebAnno is a general purpose web-based annotation tool for a wide range of linguistic annotations including various layers of morphological, syntactical, and semantic annotations.Additionaly, custom annotation layers can be defined, allowing WebAnno to be used also for non-linguistic annotation tasks.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3778

WebMetabase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0154
application sub category: topic 3375
application sub category: topic 3534
citation: bty667
citation: pubmed:30052776
description: Cleavage sites analysis tool for natural and unnatural substrates from diverse data source.
feature list: operation 3216
feature list: operation 3501
feature list: operation 3803
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: WebMetabaseManual.html

WebSpecmine
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic_0091
application sub category: topic_0092
application sub category: topic 3172
application sub category: topic 3473
application sub category: topic 3474
application sub category: topic 3489
author: Miguel Rocha
author: Sara Cardoso
author: Telma Afonso
citation: metabo9100237
citation: pmcid:PMC6835413
citation: pubmed:31635085
contributor: Marcelo Maraschin
description: WebSpecmine is a web-based application designed to perform the analysis of metabolomics data based on spectroscopic and chromatographic techniques (NMR, Infrared, UV-visible, and Raman, and LC/GC-MS)) and compound concentrations.
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: webspecmine.bio.di.uminho.pt

Webina
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic 2275
citation: https://doi.org/10.1101/2019.12.18.881789
description: An Open-Source Library and Web App that Runs AutoDock Vina Entirely in the Web Browser. 1 Abstract Molecular docking is a computational technique for predicting how a small molecule might bind a macromolecular target. Among docking programs, AutoDock Vina is particularly popular. Like many docking programs, Vina requires users to download install an executable file and to run that file from a Unix- or DOS-like command-line interface. Choosing proper configuration parameters and analyzing Vina output is also sometimes challenging. These issues are particularly problematic for students and novice researchers. We have created Webina, a new version of Vina, to address these challenges. Webina is a JavaScript WebAssembly library that runs AutoDock Vina entirely in a web browser. To use Webina, users need only visit a Webina-enabled webpage. The docking calculations take place on the user’s own computer rather than a remote server
feature list: operation_0478
feature list: operation 3454

WellInverter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic_0749
application sub category: topic 3170
citation: s12859-019-2920-4
citation: pmcid:PMC6558888
citation: pubmed:31185910
description: Web application for the analysis of fluorescent reporter gene data.
feature list: operation 1812
feature list: operation 3799
is accessible for free: true
license: Proprietary
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial WellInverter new.pdf
primary contact: Hidde de Jong
primary contact: Johannes Geiselmann

WheatCRISPR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0780
application sub category: topic 3512
application sub category: topic 3810
application sub category: topic 3912
citation: S12870-019-2097-Z
citation: pmcid:PMC6836449
citation: pubmed:31694550
description: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat. BACKGROUND:CRISPR Cas9 gene editing has become a revolutionary technique for crop improvement as it can facilitate fast and efficient genetic changes without the retention of transgene components in the final plant line. Lack of robust bioinformatics tools to facilitate the design of highly specific functional guide RNAs (gRNAs) and prediction of off-target sites in wheat is currently an obstacle to effective application of CRISPR technology to wheat improvement. DESCRIPTION:We have developed a web-based bioinformatics tool to design specific gRNAs for genome editing and transcriptional regulation of gene expression in wheat
feature list: operation_0440
feature list: operation 3096

WheatIS
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Data reference
  type: FormalParameter
  additional type: data 2093
output: Database search results
  type: FormalParameter
  additional type: data 2080
output: Identifier
  type: FormalParameter
  additional type: data_0842
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
additional type: Web application
additional type: Web service
application sub category: topic_0091
application sub category: topic_0610
application sub category: topic_0780
application sub category: topic 3071
application sub category: topic 3810
citation: s13059-018-1491-4
description: This project aims at building an International Wheat Information System (WheatIS) to support the wheat research community. The main objective is to provide a single-access web based system to access to the available data resources and bioinformatics tools. The web portal indexes and makes findable any kind of data from wheat related species. The WheatIS search is an implementation of DataDiscovery.
feature list: operation_0227
feature list: operation 2421
feature list: operation 3625
feature list: operation 3908
is accessible for free: true
license: BSD-3-Clause
software help: about
software help: help
software help: join
software help: legal
primary contact: Support service

WheatMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: Wheat IWGSC RefSeq v1.0
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest

When2Heat
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3318
citation: S41597-019-0199-Y
citation: pmcid:PMC6773861
citation: pubmed:31575870
description: Time series of heat demand and heat pump efficiency for energy system modeling. This repository contains scripts that compile heat demand and COP time series for European countries.
feature list: operation 2422
feature list: operation 3435
feature list: operation 3659
license: MIT

Whisper 2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic 3168
citation: https://doi.org/10.1101/2019.12.18.881292
description: Whisper is a tool for an accurate and high-performant mapping tool, based on the idea of sorting reads and then mapping them against suffix arrays for the reference genome and its reverse complement.
feature list: operation_0310
feature list: operation 3198
feature list: operation 3211
feature list: operation 3227
license: GPL-3.0

White blood cells detection using differential evolution (DE)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3344
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3452
description: Automatic white blood cells detector using differential evolution (DE)
feature list: operation 2429
feature list: operation 3443
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.6.0.0
primary contact: Erik

WiPP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0769
application sub category: topic 3172
application sub category: topic 3474
citation: METABO9090171
citation: pmcid:PMC6780109
citation: pubmed:31438611
description: Workflow for Improved Peak Picking for Gas Chromatography-Mass Spectrometry (GC-MS) Data | large scale GC-MS data preprocessing workflow | WiPP - A Workflow for improved Peak Picking - Quick Start Guide | WiPP is an open source large scale GC-MS data preprocessing workflow built in Python 3 that uses machine learning to optimise, automate and combine the peak detection process of commonly used peak picking algorithms
feature list: operation 3215
feature list: operation 3222
feature list: operation 3629
license: MIT

WiseNET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3474
citation: J.DIB.2019.104654
citation: pmcid:PMC6838453
citation: pubmed:31720321
description: An indoor multi-camera multi-space dataset with contextual information and annotations for people detection and tracking. Nowadays, camera networks are part of our every-day life environments, consequently, they represent a massive source of information for monitoring human activities and to propose new services to the building users. To perform human activity monitoring, people must be detected and the analysis has to be done according to the information relative to the environment and the context. Available multi-camera datasets furnish videos with few (or none) information of the environment where the network was deployed. The proposed dataset provides multi-camera multi-space video sets along with the complete contextual information of the environment. The dataset regroups 11 video sets (composed of 62 single videos) recorded using 6 indoor cameras deployed on multiple spaces
feature list: operation 3359

Wolbachia
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic 3293
application sub category: topic 3500
citation: https://doi.org/10.1101/836908
description: Complete genome assembly of the Wolbachia endosymbiont of the horn fly Haematobia irritans irritans.
feature list: operation_0525
feature list: operation 3431
feature list: operation 3840

WordCloud Cytoscape Plugin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0128
application sub category: topic_0602
application sub category: topic_0654
citation: https://doi.org/10.1186/1751-0473-6-7
citation: pmcid:PMC3083346
citation: pubmed:21473782
description: To understand the biological meaning of a cluster, the user usually has to sift through many textual annotations that are associated with biological entities. This Cytoscape plugin generates a visual summary of these annotations by displaying them as a tag cloud, where more frequent words are displayed using a larger font size. Word co-occurrence in a phrase can be visualized by arranging words in clusters or as a network.
feature list: operation 2436
feature list: operation 2497
feature list: operation 3432
feature list: operation 3501
operating system: Linux
operating system: Mac
operating system: Windows
software help: BasicTutorial
software help: ParameterTutorial
primary contact: Layla Oesper

World Cancer Map
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic 2640
application sub category: topic 3405
citation: MD.0000000000015521
citation: pmcid:PMC6531084
citation: pubmed:31096452
description: Interactive web-based platform presenting global cancer statistics , which can be used for cancer research.
feature list: operation 2429
feature list: operation 2942
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Yung-Po Liaw

WormBook
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic 2830
application sub category: topic 3512
citation: 978-1-4939-9732-9 16
citation: pubmed:31552661
description: Immunostainings in Nervous System Development of the Nematode C. elegans | Embryo series courtesy of Einhard Schierenberg | WormBook is a comprehensive, open-access collection of original, peer-reviewed chapters covering topics related to the biology of Caenorhabditis elegans and other nematodes. Wormbook also contains: WormMethods, a collection of protocols for nematode researchers; WormHistory, personal perspectives on C. elegans research; and the Worm Breeder's Gazette, an informal, non-refereed, biannual newsletter for the interchange of ideas and information related to C. elegans and other nematodes. Additional chapters can be found in GENETICS

WormBot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic_0621
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3382
citation: S11357-019-00124-9
citation: pmcid:PMC6925079
citation: pubmed:31728898
description: open-source robotics platform for survival and behavior analysis in C. elegans. WormBot, C. elegans lifespan robotic image aquisition platform. Homepage UW Pathology Seattle, Washington, USA. WormBot is an open hardware and open software robotic microscopy screening platform designed for C. elegans behavior and survival analysis. This site contains links and information for building the WormBot, an open hardware project designed for automatted survival analysis in the nematode C. elegans. The WormBot is an extremely simple and inexpensive robotics platform that captures timelapse images and realtime movies of nematodes in standard tissue culture plates
feature list: operation 3503

WormMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: Intermine data mining platform for C. elegans and related nematodes
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: 273

WormQTL2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0602
application sub category: topic_0625
citation: https://doi.org/10.1101/766386
description: an interactive platform for systems genetics in Caenorhabditis elegans | eQTL visualization and investigation | All eQTL patterns for a single trait
feature list: operation_0282
feature list: operation 3196
feature list: operation 3232

X2H
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3489
citation: TCBB.2019.2915811
citation: pubmed:31094692
description: Massive XML-based biological data management platform.
feature list: operation_0224
feature list: operation 1812
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Jian Liu
primary contact: Lei Zhang
primary contact: Qiuru Liu
primary contact: Shuhui Su
primary contact: Yongzhuang Liu

XAEM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: btz640
citation: pmcid:PMC9883676
citation: pubmed:31400221
description: Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data | Wiki for programs and pipelines for sequencing data analysis | 3. XAEM: step by step instruction and explanation | Annotation reference: XAEM requires a fasta file of transcript sequences and a gtf file of transcript annotation. XAEM supports all kinds of reference and annotation for any species. In the XAEM paper, we use the UCSC hg19 annotation:
feature list: operation 2495
feature list: operation 3501
feature list: operation 3800

XCI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0654
application sub category: topic_0659
citation: mbe.2019369
citation: pmcid:PMC7772933
citation: pubmed:31698618
description: Inferring the three-dimensional structures of the X-chromosome during X-inactivation. 3D cubic lattice, 3D structure of the X-chromosome, Xist lncRNA, X-chromosome inactivation. 3D-XCI is a lattice-based 3D modeling tool for generating accurate and stable high-resolution 3D chromosome structures based on population Hi-C data

XFlow
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic 3520
citation: https://doi.org/10.1101/2019.12.27.889253
citation: journal.pone.0227659
citation: pmcid:PMC7580946
citation: pubmed:33091000
description: An algorithm for extracting ion chromatograms.
feature list: operation 3203
feature list: operation 3636

XG-PseU
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3295
citation: S00438-019-01600-9
citation: pubmed:31392406
description: > HOMEPAGE MISSING! | an eXtreme Gradient Boosting based method for identifying pseudouridine sites | As one of the most popular post-transcriptional modifications, pseudouridine (Ψ) participates in a series of biological processes. Therefore, the efficient detection of pseudouridine sites is very important in revealing its functions in biological processes. Although experimental techniques have been proposed for identifying Ψ sites at single-base resolution, they are still labor intensive and expensive. Recently, to fill the experimental method's gap, computational methods have been proposed for identifying Ψ sites. However, their performances are still unsatisfactory. In this paper, we proposed an eXtreme Gradient Boosting (xgboost)-based method, called XG-PseU, to identify Ψ sites based on the optimal features obtained using the forward feature selection together with increment feature selection method

XGANDALF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0611
application sub category: topic 2828
application sub category: topic 3448
citation: S2053273319010593
citation: pmcid:PMC6718201
citation: pubmed:31475914
description: extended gradient descent algorithm for lattice finding | Directory Algorithm documentation | Directory precomputedSamplePoints
license: LGPL-3.0

XGBoost
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3360
application sub category: topic 3474
citation: S12864-019-6412-8
citation: pmcid:PMC6933652
citation: pubmed:31881847
description: Putative biomarkers for predicting tumor sample purity based on gene expression data.
feature list: operation 2454
feature list: operation 3463
feature list: operation 3659
license: Apache-2.0

XIBD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3168
citation: btw124
citation: pubmed:27153693
description: XIBD (X chromosome Identity by Descent) performs pairwise identity by descent (IBD) mapping on the autosomes and the X chromosome.
feature list: operation_0484
feature list: operation_0488
feature list: operation 3196
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: Lyndal Henden

XIPP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0593
application sub category: topic 3678
citation: S10858-019-00286-W
citation: pubmed:31748843
description: multi-dimensional NMR analysis software. Xipp (pronounced zip) is an NMR analysis software package created and supported by Dr. Daniel S. Garrett in the lab of Dr. G. Marius Clore. This software package is designed to study labeled proteins and nucleotides and is a complete re-write and extension of the PIPP package using Java. Xipp uses the same file format for Peak-Pick files and assignment tables as was used in PIPP. In addition many of the keyboard and mouse commands are the same as used by PIPP. The primary differences between PIPP and Xipp is that Xipp allows multiple NMR experiments to be viewed and overlayed at same and has built-in ability to aid in backbone assignment. The most important difference is that PIPP is no longer supported while Xipp is actively supported
feature list: operation_0320
feature list: operation 3214
feature list: operation 3695

XL-mHG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3678
citation: PEERJ.PREPRINTS.1962V2
citation: PEERJ.PREPRINTS.1962V3
description: XL-mHG is a Semiparametric Test for Enrichment in Ranked Lists.
feature list: operation 2238
feature list: operation 2436
feature list: operation 3799
license: BSD-3-Clause

XTRACT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3067
application sub category: topic 3304
application sub category: topic 3337
application sub category: topic 3384
application sub category: topic 3444
citation: https://doi.org/10.1101/804641
description: Standardised protocols for automated tractography and connectivity blueprints in the human and macaque brain. WM tract atlases for the human (HCP and UK Biobank) and Macaque brain and connectivity blueprint atlases for the human (HCP) and macaque brain. Reference: Warrington S, Bryant KL, Khrapitchev AA, Sallet J, Charquero-Ballester M, Douaud G, Jbabdi S, Mars RB*, Sotiropoulos SN* (in prep.) XTRACT - Standardised protocols for automated tractography and connectivity blueprints in the human and macaque brain. XTRACT - a command-line tool for automated tractography. XTRACT can be used to automatically extract a set of carefully dissected tracts in humans and macaques (other species to come). It can also be used to define one's own tractography protocols where all the user needs to do is to define a set of masks in standard space (e.g. MNI152)
feature list: operation 3435

XenMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Query script
  type: FormalParameter
  additional type: data 3786
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: Search and retrieve integrated Xenopus tropicalis and Xenopus laevis data
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: b BETA bUpdated on:Sep-02-2015

XenoCP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0099
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3304
application sub category: topic 3673
citation: https://doi.org/10.1101/843250
description: Cloud-based BAM cleansing tool for RNA and DNA from Xenograft. A cloud-based tool for mouse read cleansing in xenograft samples. XenoCP is a tool for cleansing mouse reads in xenograft BAMs. XenoCP can be easily incorporated into any workflow, as it takes a BAM file as input and efficiently cleans up the mouse contamination. The output is a clean human BAM file that could be used for downstream genomic analysis. St. Jude Children's Research Hospital - Pediatric Cancer Genomic Data Portal. Your web browser (Chrome 68) is out of date. Update your browser for more security, speed and the best experience on this site. Update browser Ignore
feature list: operation 2495
feature list: operation 3198
feature list: operation 3800
license: Apache-2.0

Xeva
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0208
application sub category: topic 2640
application sub category: topic 3360
citation: 0008-5472.CAN-19-0349
citation: pubmed:31142512
description: Integrative pharmacogenomics analysis of patient-derived xenografts.
feature list: operation_0533
feature list: operation 3501
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: Xeva.pdf
primary contact: Benjamin Haibe-Kains

XitoSBML
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2229
application sub category: topic 2259
application sub category: topic 3382
citation: FGENE.2019.01027
citation: pmcid:PMC6842926
citation: pubmed:31749833
description: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images. XitoSBML - the spatial SBML plugin for ImageJ. XitoSBML: Spatial SBML Plugin for ImageJ. XitoSBML is an ImageJ plugin which creates a Spatial SBML model from segmented images. XitoSBML is not just a converter, but also a spatial model editor so that users can add molecules(species), reactions, and advection/diffusion coefficients to the converted Spatial SBML model
feature list: operation 2426
feature list: operation 3443
license: Apache-2.0

Xylella
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0632
application sub category: topic_0780
application sub category: topic 3168
application sub category: topic 3174
citation: https://doi.org/10.1101/810648
description: Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material.
feature list: operation 3472
feature list: operation 3840

YALFF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3168
citation: S12859-019-2883-5
citation: pmcid:PMC6873394
citation: pubmed:31757199
description: Better quality score compression through sequence-based quality smoothing. YALFF (Yet Another Lossy FASTQ Filter) is a smoother for FASTQ files which uses an FM-Index to store the k-mer database. The compressed index greatly reduces the amount of memory required compared to other tools such as QUARTZ. This is because the dictionary of k-mers can be linearized into contigs
feature list: operation_0484
feature list: operation 3196
feature list: operation 3211
feature list: operation 3472
license: MIT

YAPP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic 3168
application sub category: topic 3512
citation: S40246-019-0219-1
citation: pmcid:PMC6670153
citation: pubmed:31366376
description: Identification of a novel long non-coding RNA within RUNX1 intron 5 | This site uses cookies. By continuing to browse the site you are agreeing to our use of cookies. Find out more here . {{alert.msg}}
feature list: operation_0440
feature list: operation_0441
feature list: operation 2495

Yanagi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3320
citation: S12859-019-2947-6
citation: pmcid:PMC6693274
citation: pubmed:31409274
description: Fast and interpretable segment-based alternative splicing and gene expression analysis | Transcript Segment Library Construction for RNA-Seq Quantification | Analysis of differential alternative splicing from RNA-seq data is complicated by the fact that many RNA-seq reads map to multiple transcripts, and that annotated transcripts from a given gene are often a small subset of many possible complete transcripts for that gene
feature list: operation 2495
feature list: operation 3223
feature list: operation 3800

YeastMine
type: SoftwareApplication
input: Ontology data
  type: FormalParameter
  additional type: data 2353
input: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Sequence features
  type: FormalParameter
  additional type: data 1255
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: Search and retrieve S. cerevisiae data, populated by SGD and powered by InterMine
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: Data Updated on: Nov-19-2019

YeastSpotter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3068
application sub category: topic 3382
citation: btz402
citation: pmcid:PMC6821424
citation: pubmed:31095270
description: Accurate and parameter-free web segmentation for microscopy images of yeast cells.
feature list: operation 3552
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: FAQ
primary contact: Alan Moses
primary contact: Alex Lu

Yersinia
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic_0632
application sub category: topic 3168
application sub category: topic 3293
application sub category: topic 3305
citation: MGEN.0.000301
citation: pmcid:PMC6861861
citation: pubmed:31580794
description: Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization.
feature list: operation 3192
feature list: operation 3431
feature list: operation 3460
feature list: operation 3840

Yosshi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic_0130
application sub category: topic_0623
application sub category: topic_0821
citation: GKZ385
citation: pmcid:PMC6602428
citation: pubmed:31106356
description: Yosshi (YOur web-server for S-S bond HarvestIng) - web server for disulfide engineering by bioinformatic analysis of diverse protein families.
feature list: operation_0303
feature list: operation_0471
feature list: operation 1850
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: yosshi
primary contact: Dmitry Suplatov

Yvis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0152
application sub category: topic_0154
application sub category: topic 2830
citation: GKZ387
citation: pmcid:PMC6602444
citation: pubmed:31106372
description: Antibody high-density alignment visualization and analysis platform with an integrated database.
feature list: operation 3431
feature list: operation 3695
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: https://orcid.org/0000-0001-7776-8446
primary contact: Liza F Felicori

ZebraSTM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0611
application sub category: topic 2840
application sub category: topic 3304
citation: zeb.2018.1688
citation: pubmed:30615594
description: Application for quantification of spontaneous tail movement in zebrafish embryos.
feature list: operation 3799
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Ulises Bardullas

ZebrafishMine
type: SoftwareApplication
input: Sequence features
  type: FormalParameter
  additional type: data 1255
input: Ontology data
  type: FormalParameter
  additional type: data 2353
output: Over-representation data
  type: FormalParameter
  additional type: data 3753
output: Query script
  type: FormalParameter
  additional type: data 3786
output: Sequence features
  type: FormalParameter
  additional type: data 1255
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
additional type: Web service
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic 3071
citation: bts577
citation: pmcid:PMC3516146
citation: pubmed:23023984
description: ZebrafishMine is powered by the InterMIne data warehouse system, and integrates biological data sets from multiple sources. It currently includes updates of data from ZFIN, the zebrafish model organism database. There is also data from the Panther database.
feature list: operation_0224
feature list: operation_0337
feature list: operation 2422
feature list: operation 2436
is accessible for free: true
license: LGPL-2.1
operating system: Linux
operating system: Mac
software help: web-services
software help: latest
software version: Last Build: 03.28.2013

Zebrafish neuroanatomy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
description: Zebrafish is an online database of standardized Zebrafish (a marine vertebrate model) neuroanatomy, accessible via an interactive interface for 3D visualisation.
feature list: operation_0337

ZincBind
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web API
additional type: Web application
application sub category: topic_0749
application sub category: topic 3489
application sub category: topic 3534
citation: baz006
citation: pmcid:PMC6361820
citation: pubmed:30722040
description: Database of zinc binding sites.
feature list: operation_0389
feature list: operation_0445
feature list: operation 2575
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
primary contact: Sam Ireland

Zirmi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic_0769
application sub category: topic 3382
citation: JBM.2018.259
citation: pmcid:PMC6706154
citation: pubmed:31453251
description: An automated quantitative image analysis pipeline of in vivo oxidative stress and macrophage kinetics | Zebrafish leukocyte tracking pipeline in Matlab | Zebrafish leukocyte tracking pipeline in Matlab. Version 1.4
feature list: operation 3799

Zombi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
citation: btz710
citation: pmcid:PMC7031779
citation: pubmed:31566657
description: A phylogenetic simulator of trees, genomes and sequences that accounts for dead linages | Evolution simulator with extinct lineages | Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages | Zombi is a flexible platform of genome evolution which can be of great interest to those who want to test different evolutionary hypotheses under simulations and need to use a fast and easy-to-use tool to generate species trees, gene trees or sequences. Zombi's output is especially simple and easy to read, understand and parse
feature list: operation_0325
feature list: operation_0544
feature list: operation 3478

ZooScatR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0621
application sub category: topic 3452
citation: https://doi.org/10.1121/1.5085655
citation: pubmed:30710911
description: R package for modelling the scattering properties of weak scattering targets using the distorted wave Born approximation.
feature list: operation_0337
feature list: operation 3435
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Australian Antarctic Division

Zr-MOFs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 2828
application sub category: topic 3489
citation: ACSAMI.9B17885
citation: pubmed:31738502
description: Large-Scale Structural Refinement and Screening of Zirconium Metal-Organic Frameworks for H2S/CH4 Separation. You can find more than 182 experimentally synthesized guest-free and disorder-free Zirconium-based metal-organic frameworks (Zr-MOFs), which contain no less than 10 coordinated Zr6O8 inner cores. These structures are optimized by a combination of periodic density functional theory (DFT) and molecular mechanics method, and are given in cif format
feature list: operation 2422

A-DaGO-Fun
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
citation: btv590
citation: pmcid:PMC5006308
citation: pubmed:26476781
description: Python library that provides a comprehensive and customized set of Gene Ontology (GO) based functional analysis tools that exploit the biological knowledge that GO offers in describing genes or groups of genes through the use of GO semantic similarity measures for biological knowledge discovery.
feature list: operation 2436
operating system: Linux
software help: adagofun

A-GAME
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
citation: s12864-017-4369-z
citation: pmcid:PMC5767027
citation: pubmed:29329522
description: A web service incorporating state of the art tools and workflows for the analysis of eDNA sequence data. Dedicated tools available in A-GAME allow efficient analysis of pooled libraries and rapid identification of candidate genes, reducing sequencing costs and saving the need for laborious manual annotation.
feature list: operation 3672
provider: ELIXIR-ITA-MILANO
software version: 1
primary contact: https://orcid.org/0000-0002-6739-2657

A-HIOT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 3047
application sub category: topic 3336
application sub category: topic 3474
citation: s13321-022-00630-7
citation: pmcid:PMC9306080
citation: pubmed:35869511
description: A method that simultaneously identifies and optimizes hit/lead molecules by integrating chemical- and protein-space-driven architectures and stands for an automated-hit identification and optimization tool (A-HIOT).
feature list: operation 2422
feature list: operation 3935
feature list: operation 3938
license: Not licensed

A-ITR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3315
application sub category: topic 3360
application sub category: topic 3401
application sub category: topic 3474
application sub category: topic 3577
citation: pmcid:PMC8324003
citation: pubmed:34335111
description: This R package is designed for computing alternative individualized treatment recommendation (A-ITR).
feature list: operation 3435
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

A-MADMAN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0203
citation: https://doi.org/10.1186/1471-2105-10-201
citation: pmcid:PMC2711946
citation: pubmed:19563634
description: Open source web application and gene chip analysis automation framework for annotation-based meta-analysis of data from public repositories (NCBI GEO). It allows retrieval, annotation, organization and analysis of gene expression data from public repository. It automates several analysis steps to be accomplished to setup a working environment for conducting meta-analyses, without giving up power and flexibility.
feature list: operation 2495
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: ELIXIR-ITA-PADOVA
software help: general.html
software version: 1.4
primary contact: Andrea Bisognin
primary contact: Stefania Bortoluzzi

a-o-tool
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3170
application sub category: topic 3308
citation: S12920-019-0524-5
citation: pmcid:PMC6533699
citation: pubmed:31122257
description: Exploiting orthology and de novo transcriptome assembly to refine target sequence information.
feature list: operation_0476
feature list: operation 3258
feature list: operation 3644
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
primary contact: https://orcid.org/0000-0002-2585-3830

A-PASS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0769
application sub category: topic 3304
application sub category: topic 3444
citation: ac83f2
citation: pubmed:35878599
description: A pipeline to automatically process and analyze simultaneously acquired EEG-fMRI data for sleep research
is accessible for free: true
license: Not licensed

A-Prot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0082
application sub category: topic_0123
application sub category: topic 2814
application sub category: topic 3474
citation: S12859-022-04628-8
citation: pmcid:PMC8925138
citation: pubmed:35296230
description: Protein structure modeling using MSA transformer
feature list: operation_0267
feature list: operation_0272
feature list: operation_0303
feature list: operation_0477
feature list: operation_0492
license: CC-BY-NC-SA-4.0

A-SOID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3474
citation: https://doi.org/10.1101/2022.11.04.515138
description: An active learning platform for expert-guided, data efficient discovery of behavior
license: BSD-3-Clause-Clear

A2A
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3068
application sub category: topic 3303
application sub category: topic 3379
citation: S12859-020-03894-8
citation: pmcid:PMC7751125
citation: pubmed:33349237
description: A platform for research in biomedical literature search and benchmarking.
feature list: operation_0305
feature list: operation 1812
feature list: operation 2422
software help: about

A2Sign
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0632
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3518
citation: BTAB773
citation: pubmed:34788798
description: A2Sign (Agnostic Algorithms for Signatures) a universal method for identifying molecular signatures from transcriptomic datasets prior to cell-type deconvolution.
feature list: operation_0314
feature list: operation 3629
feature list: operation 3802
license: MIT
primary contact: Franck Augé

A2TEA
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 1929
input: Sequence features
  type: FormalParameter
  additional type: data 1255
  encoding format: format 2306
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
output: Phylogenetic tree
  type: FormalParameter
  additional type: data_0872
output: GO-term enrichment data
  type: FormalParameter
  additional type: data 3754
output: Gene expression profile
  type: FormalParameter
  additional type: data_0928
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
additional type: Workflow
application sub category: topic_0084
application sub category: topic_0121
application sub category: topic_0203
application sub category: topic_0769
application sub category: topic_0780
application sub category: topic 3170
application sub category: topic 3308
citation: F1000RESEARCH.126463.2
citation: pmcid:PMC10186066
citation: pubmed:37224329
description: A2TEA is a software workflow facilitating identification of candidate genes for stress adaptation based on comparative genomics and transcriptomics. It combines differential gene expression with gene family expansion as an indicator for the evolution of adaptive traits.
feature list: operation_0337
feature list: operation 3192
feature list: operation 3223
feature list: operation 3431
feature list: operation 3501
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

A3D Database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0130
application sub category: topic_0166
application sub category: topic_0736
citation: https://doi.org/10.1101/2021.11.17.468872
description: A3D Database is a database for structure-based protein aggregation predictions for the human proteome
feature list: operation_0408
feature list: operation_0409
feature list: operation_0474
feature list: operation 3436
feature list: operation 4008
is accessible for free: true

A3DyDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0130
application sub category: topic_0621
application sub category: topic_0736
citation: s12934-023-02182-3
citation: pmcid:PMC10504709
citation: pubmed:37716955
description: Exploring structural aggregation propensities in the yeast proteome.
feature list: operation_0303
feature list: operation_0408
feature list: operation_0409
feature list: operation 3436
feature list: operation 4008
is accessible for free: true

A3FE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0749
application sub category: topic_0769
application sub category: topic 3336
citation: ACS.JCTC.4C00806
citation: pmcid:PMC11428140
citation: pubmed:39254715
description: A3FE is an open-source package implementing an automated workflow for alchemical absolute binding free energy calculations, designed to reduce computational cost and human intervention.
feature list: operation 3435
feature list: operation 3938

a4
type: SoftwareApplication
input: Processed microarray data
  type: FormalParameter
  additional type: data 3111
  encoding format: format 2056
input: Sample annotation
  type: FormalParameter
  additional type: data 3113
  encoding format: format 3751
output: Sample annotation
  type: FormalParameter
  additional type: data 3113
  encoding format: format 3751
output: Processed microarray data
  type: FormalParameter
  additional type: data 3111
  encoding format: format 2056
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 2269
application sub category: topic 3518
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: Suite of R packages for analysis of Affymetrix microarray experiments.
feature list: operation 2238
feature list: operation 2409
feature list: operation 2495
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: a4.html
software version: 1.22.0
primary contact: Tobias Verbeke
primary contact: Willem Ligtenberg

a4Base
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 2269
application sub category: topic 3518
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: An R package of the "a4" packages collection. It comprises of basic funtionalities needed to analyse Affymetrix microarray experiment results.
feature list: operation_0337
feature list: operation 2238
feature list: operation 2495
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: a4Base.html
software version: 1.22.0
primary contact: Tobias Verbeke
primary contact: Willem Ligtenberg

a4Classif
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3473
application sub category: topic 3518
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: An R package of the "a4" packages collection. It comprises of commands using machine learning algorithms for classification work to analyse Affymetrix microarray experiment results.
feature list: operation 2238
feature list: operation 2990
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: a4Classif.html
software version: 1.22.0
primary contact: Tobias Verbeke
primary contact: Willem Ligtenberg

a4Core
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3071
application sub category: topic 3518
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: An R package of the "a4" packages collection. It is made to allow for easy interopetability with the nlcv R package.
feature list: operation 2238
feature list: operation 2409
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: a4Core.html
software version: 1.22.0
primary contact: Tobias Verbeke
primary contact: Willem Ligtenberg

Aggrescan4D
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0108
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic_0736
citation: GKAE382
citation: pmcid:PMC11223845
citation: pubmed:38738618
description: Aggrescan4D (A4D) is a web server for predicting pH-dependent protein aggregation and engineering protein solubility. It builds on the A3D method, offering evolutionary-informed mutation protocols and integrating precalculated results and structure retrieval from AlphaFold.
feature list: operation_0303
feature list: operation_0400
feature list: operation_0409
feature list: operation 3436
feature list: operation 4008

a4Preproc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0089
application sub category: topic 3518
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: An R package of the "a4" packages collection. It is used for microarray data preprocessing where annotation information is added to experimental result data.
feature list: operation_0226
feature list: operation 2238
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: a4Preproc.html
software version: 1.22.0
primary contact: Tobias Verbeke
primary contact: Willem Ligtenberg

a4Reporting
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 1775
application sub category: topic 3518
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: An R package of the "a4" packages collection. It provides reporting functionality.
feature list: operation_0361
feature list: operation 2238
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: a4Reporting.html
software version: 1.22.0
primary contact: Tobias Verbeke
primary contact: Willem Ligtenberg

A5
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
citation: journal.pone.0042304
citation: pmcid:PMC3441570
citation: pubmed:23028432
description: A5 is an integrative pipeline for genome assembly that automates sequence data cleaning, error correction, assembly, and quality control by chaining a number of programs together with additional custom algorithms.
feature list: operation_0524
license: GPL-3.0
operating system: Linux
operating system: Mac
software help: browse pages
primary contact: Aaron E. Darling

A5-miseq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
citation: pubmed:25338718
description: De novo assembly & analysis of Illumina sequence data, including the A5 pipeline, A5-miseq, tools to evaluate assembly quality, and scripts to facilitate data submission to NCBI and the RAST annotation system
feature list: operation_0310
feature list: operation_0524
feature list: operation 3431
operating system: Linux
operating system: Mac
software help: ngopt

aCLImatise
type: SoftwareApplication
input: Text data
  type: FormalParameter
  additional type: data 2526
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 3857
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
description: aCLImatise is a Python library and command-line utility for parsing the help output of a command-line tool and then outputting a description of the tool in a more structured format, for example a Common Workflow Language tool definition.
feature list: operation 1812
is accessible for free: true
license: GPL-3.0
operating system: Linux
software help: CliHelpParser
software version: 2.2.0

aFold
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3518
citation: S12864-019-5686-1
citation: pmcid:PMC6509820
citation: pubmed:31077153
description: Using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data.
feature list: operation 3223
feature list: operation 3680
feature list: operation 3800
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ABSSeq.pdf
primary contact: 0000-0002-1413-913X
primary contact: Wentao Yang

A_Purva
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0080
citation: cmb.2009.0196
citation: pubmed:21210730
description: Contact Map Overlap maximization (CMO) solver. Given two protein structures represented by two contact maps, it computes the amino-acid alignment which maximize the number of common contacts.
feature list: operation 2451
operating system: Linux
operating system: Mac
software help: manual.pdf
software version: 1

AA-Score
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 3336
citation: acs.jcim.1c01537
citation: pubmed:35452230
description: A command line tool for protein-ligand binding affinity prediction
feature list: operation_0394
feature list: operation 1839
feature list: operation 3938
is accessible for free: true
license: GPL-2.0
operating system: Linux

AA_stat
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0601
application sub category: topic 3520
citation: https://doi.org/10.1101/2020.09.07.286161
description: AA_stat is a tool for shotgun proteomics that uncovers the unexpected modifications of amino acid residues in the protein sequences, as well as possible artefacts of data acquisition or processing, in the results of proteome analysis.
feature list: operation_0417
feature list: operation 3215
feature list: operation 3638
feature list: operation 3649
feature list: operation 3755
software help: aa stat report example

AAAKB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 2885
application sub category: topic 3474
citation: journal.pone.0289966
citation: pmcid:PMC10723669
citation: pubmed:38100461
description: A manually curated database for tracking and predicting genes of Abdominal aortic aneurysm (AAA).
feature list: operation 2436
feature list: operation 2437
feature list: operation 2454
feature list: operation 2492
feature list: operation 3223
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

AACompIdent
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic 3520
citation: nbt0196-61
citation: pubmed:9636313
description: Protein identification by amino acid composition, and optionally pI, Mw, species, UniProtKB keyword and calibration protein. Several constellations are available, corresponding to various amino acid analysis techniques.
feature list: operation 2479
operating system: Linux
operating system: Mac
operating system: Windows
software help: aacomp-doc.html
primary contact: ExPASy helpdesk

AACompSim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic 1775
citation: nbt0196-61
citation: pubmed:9636313
description: Compare amino acid composition of a UniProtKB entry with some or all other UniProtKB entries. Several constellations are available, corresponding to various amino acid analysis techniques.
feature list: operation 2479
operating system: Linux
operating system: Mac
operating system: Windows
software help: aacsim-doc.html
primary contact: ExPASy helpdesk

AACon
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0080
description: Set of tools implementing different conservation scores.
feature list: operation 2479
operating system: Linux
operating system: Mac
operating system: Windows
software help: aacon
software version: 1

AADB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 3068
application sub category: topic 3172
application sub category: topic 3305
citation: tcbb.2023.3283221
citation: pubmed:37279138
description: Manually collected database for combinations of antibiotics with adjuvants.
feature list: operation 2421
feature list: operation 3482
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

AADG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3384
application sub category: topic 3474
citation: tmi.2022.3193146
citation: pubmed:35862336
description: Automated Augmentation for Domain Generalization (AADG) is a data manipulation based domain generalization method that can sample data augmentation policies that generate domains and diversify the training set from an appropriate search space.
feature list: operation 2428
feature list: operation 3799
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

AAgAtlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 2830
application sub category: topic 3068
application sub category: topic 3360
citation: 978-1-0716-0389-5 21
citation: pubmed:32162267
description: AAgAtlas is a database of human autoantigens extracted from biomedical literature.
feature list: operation 2421
feature list: operation 2422
software version: 1.0

AagingBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic 3300
application sub category: topic 3399
application sub category: topic 3407
application sub category: topic 3930
citation: baae016
citation: pmcid:PMC10930205
citation: pubmed:38470883
description: A comprehensive database of anti-aging peptides.
feature list: operation_0495
feature list: operation 2421
feature list: operation 3631
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

aaindexextract
type: SoftwareApplication
input: Amino acid index
  type: FormalParameter
  additional type: data 1501
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
citation: S0168-9525(00)02024-2
citation: CBO9781139151399
citation: CBO9781139151405
contributor: EMBOSS Contributors
contributor: UK BBSRC
contributor: UK MRC
contributor: Wellcome Trust
description: Extract amino acid property data from AAINDEX.
feature list: operation 1812
funder: UK BBSRC
funder: UK MRC
funder: Wellcome Trust
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
provider: EMBOSS
software help: ch01s01.html
software help: pr02s04.html
software help: aaindexextract.html
software version: r6

AAIndexLoc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0140
citation: s00726-007-0616-y
citation: pubmed:18163182
description: Machine-learning-based algorithm that uses amino acid index to predict protein subcellular localization based on its sequence.
feature list: operation 2479
feature list: operation 2489
operating system: Linux
operating system: Mac
operating system: Windows
software help: aaindexloc.bii.a-star.edu.sg

AAindexNC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0123
application sub category: topic_0154
application sub category: topic_0736
application sub category: topic_0821
application sub category: topic 2275
citation: IJMS252312555
citation: pmcid:PMC11641631
citation: pubmed:39684267
description: AAindexNC is a bioinformatics tool and database that estimates the physicochemical properties of non-canonical amino acids derived from protein structures and the PDBechem databank, building upon the existing AAindex database.
feature list: operation_0250
feature list: operation_0267
feature list: operation_0474
feature list: operation_0478
feature list: operation 3659

AARDVARK
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic_0622
application sub category: topic_0654
application sub category: topic 3676
citation: btad509
citation: pmcid:PMC10457659
citation: pubmed:37584701
description: AARDVARK is an R package that identifies reversion mutations in DNA sequence data.
feature list: operation_0292
feature list: operation 3198
feature list: operation 3227
is accessible for free: true
license: MIT

AARNet FileSender
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: FileSender is an open source web application for sending files of any size, quickly and securely. FileSender is available to all institutions affiliated with the Australian Access Federation (AAF). You can use your institution login details to access and use FileSender.
license: BSD-3-Clause
software help: filesender
software help: https://www.aarnet.edu.au/news-events

AASRA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Workflow
application sub category: topic_0097
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3512
citation: ioab062
citation: pmcid:PMC8256102
citation: pubmed:33787835
description: The Anchor Alignment-Based Small RNA Annotation (AASRA) Pipeline is a comprehensive solution for small RNA alignment.
feature list: operation_0292
feature list: operation_0463
feature list: operation 3192
feature list: operation 3198
feature list: operation 3799
license: GPL-1.0

AASsites
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2885
citation: 1471-2105-12-s4-s2
citation: pmcid:PMC3194194
citation: pubmed:21992029
description: Automated bioinformatics pipeline to analyse SNP containing DNA sequences mainly for finding SNPs which cause a change in the splicing pattern.
feature list: operation_0484
operating system: Linux
operating system: Mac
operating system: Windows
software help: aassites

AAstretch
type: SoftwareApplication
input: Sequence record
  type: FormalParameter
  additional type: data_0849
  encoding format: format 1219
output: Comparison matrix
  type: FormalParameter
  additional type: data_0874
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0080
application sub category: topic 3299
author: Matteo Ramazzotti - matteo dot ramazzotti at unifi.it
citation: journal.pone.0030824
citation: pmcid:PMC3270027
citation: pubmed:22312432
description: It is a suite of perl scripts aimed at scannig a properly formatted set of protein sequences and their corresponding coding sequences and extract from them imperfect homopetidic repeats of a given amino acid. The user can define the nature of such residue and the maximal length and proportion of insertions tolerated, together with other search parameters.
feature list: operation_0236
feature list: operation_0379
operating system: Linux
operating system: Mac
operating system: Windows
provider: ELIXIR-ITA-FIRENZE
software version: 1.0
primary contact: Matteo Ramazzotti

AAU-net
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3954
citation: tmi.2022.3226268
citation: pubmed:36455083
description: An adaptive attention U-net (AAU-net) to segment breast lesions automatically and stably from ultrasound images.
license: Not licensed

AB-Amy
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
  encoding format: format 1957
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0621
application sub category: topic_0634
application sub category: topic 2830
application sub category: topic 3377
application sub category: topic 3474
citation: TBAD007
citation: pmcid:PMC10365155
citation: pubmed:37492587
description: Machine learning aided amyloidogenic risk prediction of therapeutic antibody light chains.
feature list: operation 2475
feature list: operation 3431
feature list: operation 3436
is accessible for free: true
license: CC-BY-NC-4.0
operating system: Linux
operating system: Mac
operating system: Windows

Ab-CoV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0154
application sub category: topic_0199
application sub category: topic_0219
application sub category: topic 2830
citation: BTAC439
citation: pubmed:35771624
description: A curated database for binding affinity and neutralization profiles of coronavirus related antibodies.
feature list: operation_0331
feature list: operation_0337
feature list: operation_0416
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows
software help: help

Ab-Ligity
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0605
application sub category: topic 2275
application sub category: topic 2830
citation: https://doi.org/10.1101/2020.03.24.004051
description: Identifying sequence-dissimilar antibodies that bind to the same epitope.
feature list: operation_0303
feature list: operation_0416
feature list: operation_0478
feature list: operation 3196
license: BSD-3-Clause
primary contact: https://orcid.org/0000-0003-1388-2252

AB12PHYLO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic_0084
application sub category: topic_0769
application sub category: topic 3168
citation: https://doi.org/10.1101/2021.03.01.433007
description: AB12PHYLO is an integrated pipeline for Maximum Likelihood phylogenetic inference from ABI trace data.
feature list: operation_0323
feature list: operation_0326
feature list: operation 3192
feature list: operation 3196
license: GPL-3.0
software help: Commandline-Tutorial
software help: Graphical-Tutorial
software help: Installation
primary contact: https://orcid.org/0000-0002-3444-6954

abacas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
citation: btp347
description: ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly contigs against the reference. The output is then processed to generate a pseudomolecule taking overlaping contigs and gaps in to account. MUMmer's alignment generating programs, Nucmer and Promer are used followed by the 'delta-filter' utility function. Users could also run tblastx on contigs that are not used to generate the pseudomolecule.
feature list: operation_0310
software help: documentation.html
software version: 1.1

ABACUS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0622
citation: btt697
citation: pubmed:24292361
description: Identify SNPs significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions. Applied to a whole SNP dataset, the tool gives as output a list of SNP-sets associated with the disease and, for each SNP-set, the list of significant SNPs.
feature list: operation 2497
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: ELIXIR-ITA-PADOVA
software help: ABACUS
software version: 1.2
primary contact: Barbara Di Camillo

AbAdapt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2275
application sub category: topic 2830
citation: vbac015
citation: pmcid:PMC9710585
citation: pubmed:36699363
description: Approach to predicting antibody-antigen complex structures from sequence.
feature list: operation_0252
feature list: operation_0416
feature list: operation_0478
feature list: operation_0480
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

ABAEnrichment
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 3304
citation: btw392
citation: pmcid:PMC5048072
citation: pubmed:27354695
description: The package is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function 'aba_enrich' integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. 'aba_enrich' interfaces the ontology enrichment software FUNC to perform the statistical analyses.
feature list: operation 2436
license: GPL-2.0
operating system: Mac
operating system: Windows
software help: ABAEnrichment.html
software version: 1.4.0
primary contact: Steffi Grote

AbAgIntPre
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0621
application sub category: topic 2830
application sub category: topic 3474
application sub category: topic 3930
citation: fimmu.2022.1053617
citation: pmcid:PMC9813736
citation: pubmed:36618397
description: A deep learning method for predicting antibody-antigen interactions based on sequence information.
feature list: operation_0252
feature list: operation_0416
feature list: operation_0478
feature list: operation_0480
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows

Abalign
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic 2830
application sub category: topic 3168
application sub category: topic 3930
application sub category: topic 3948
citation: gkad400
citation: pmcid:PMC10320167
citation: pubmed:37207341
description: A comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires.
feature list: operation_0292
feature list: operation_0416
feature list: operation_0553
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

abalonedb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0121
application sub category: topic 3293
application sub category: topic 3308
citation: G3.119.400388
citation: pmcid:PMC6778792
citation: pubmed:31413154
description: The Abalomics community portal is a community driven project to increase genetic knowledge of the abalone species.
feature list: operation 3192
feature list: operation 3216

ABarray
type: SoftwareApplication
input: Gene expression data
  type: FormalParameter
  additional type: data 2603
  encoding format: format 3751
input: Resource metadata
  type: FormalParameter
  additional type: data 2337
  encoding format: format 3751
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 3617
output: Mathematical model
  type: FormalParameter
  additional type: data_0950
  encoding format: format 2032
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic_0769
application sub category: topic 2269
application sub category: topic 3518
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: An R package which functions provide an automated pipeline to perform expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis. A GUI interface is also provided.
feature list: operation_0337
feature list: operation 2238
feature list: operation 2409
feature list: operation 2428
feature list: operation 2495
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ABarray.html
software version: 1.42.0
primary contact: Yongming Andrew Sun

Abasy Atlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0114
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic 3895
citation: https://doi.org/10.1101/2020.05.04.077420
description: Abasy (Across-bacteria systems) Atlas contains the most comprehensive collection of reconstructed and meta-curated bacterial gene regulatory networks having enough quality to allow system-level analyses.
feature list: operation_0438
feature list: operation 1781
feature list: operation 2437
feature list: operation 3431

abawaca
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3174
citation: nature14486
citation: pubmed:26083755
description: abawaca (A Binning Algorithm Without A Cool Acronym) is a binning program that can take advantage of different types of information such as differential coverage and DNA signature.
feature list: operation 3798
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
software help: README.html

ABBA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic 3168
application sub category: topic 3174
citation: journal.pcbi.1000186
citation: pubmed:18818729
description: Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly.
feature list: operation_0523
feature list: operation_0525
feature list: operation 3216
is accessible for free: true
license: Artistic-2.0
operating system: Linux

ABC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 3169
citation: btv321
citation: pmcid:PMC4668780
citation: pubmed:25995231
description: Computational tool that identifies allele specific binding of transcription factors from aligned ChIP-Seq reads at heterozygous SNVs.
feature list: operation_0445
operating system: Linux
operating system: Mac
software help: ABC

ABC-finder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic_0736
application sub category: topic_0769
application sub category: topic 3300
citation: https://doi.org/10.1101/2020.11.18.042887
description: A containerized web server for the identification and topology prediction of ABC proteins. ABC-Finder i.e., A Docker-based package for the identification of ABC proteins in all organisms, and downstream analysis and visualization of the topology of ABC proteins using an interactive web browser.
feature list: operation_0303
feature list: operation_0337
feature list: operation 3767
license: GPL-3.0

ABC-GWAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0749
application sub category: topic 2640
application sub category: topic 2885
application sub category: topic 3173
application sub category: topic 3517
citation: FGENE.2020.00730
citation: pmcid:PMC7379852
citation: pubmed:32765587
description: A web application for analysis of breast cancer GWAS variants.
feature list: operation 3196
feature list: operation 3226
feature list: operation 3431
feature list: operation 3661

abc4pwm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0128
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3170
application sub category: topic 3179
citation: S12859-022-04615-Z
citation: pmcid:PMC8896320
citation: pubmed:35240993
description: abc4pwm is a software tool for clustering of pwms, classficiation of pwms to their DNA binding Domain, motif search, and other supportive modules.
feature list: operation_0238
feature list: operation_0239
feature list: operation 3192
feature list: operation 3432
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac

ABC-HuMi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3174
application sub category: topic 3277
application sub category: topic 3697
citation: gkad1086
citation: pmcid:PMC10767846
citation: pubmed:37994699
description: The atlas of biosynthetic gene clusters in the human microbiome.
feature list: operation_0337
feature list: operation 2421
feature list: operation 3432
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

ABC portal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3308
application sub category: topic 3400
application sub category: topic 3408
citation: gkac646
citation: pmcid:PMC9825444
citation: pubmed:35920330
description: ABC portal provides web-based interactive analysis modules, especially a comprehensive cell-cell communication analysis and disease-related gene signature analysis.
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

AbCD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic 3056
citation: btt041
citation: pmcid:PMC3597143
citation: pubmed:23357921
contributor: http://orcid.org/0000-0002-5643-2668
description: Providides pre-estimated effective sample sizes, specific to each minor allele frequency (MAF) category, for designs with arbitrary coverage (0.5 - 30X) and sample size (20-20,000), and for four major ethnic groups (Europeans, Africans, Asians and African Americans).
feature list: operation 2422
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows
software help: abcd.tutorial.html

Alzheimers Disease Biomarker Comprehensive Database (ABCD)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 3360
citation: S13205-019-1888-0
citation: pmcid:PMC6722159
citation: pubmed:31501752
description: An Alzheimer's Disease Biomarker Comprehensive Database for Humans. It includes the information for all the genetic parameters like mitochondrial genes, polymorphic genes (SNP's), transcription factors, proteins, miRNAs, Associative pathway, and AD brain images.
feature list: operation 2495
feature list: operation 3501

Aliment to Bodily Condition knowledgebase (ABCkb)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Workbench
application sub category: topic_0218
application sub category: topic_0602
application sub category: topic_0780
application sub category: topic 3390
application sub category: topic 3810
citation: https://doi.org/10.1101/2021.03.20.436160
description: The Aliment to Bodily Condition knowledgebase (ABCkb) is a database connecting plants and human health.
feature list: operation 1812
feature list: operation 2421
license: GPL-3.0

ABCModeller
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2269
application sub category: topic 3473
application sub category: topic 3474
citation: BBAA247
citation: pubmed:33057581
description: An automatic data mining tool based on a consistent voting method with a user-friendly graphical interface. In order to extract useful information from a huge amount of biological data nowadays, simple and convenient tools are urgently needed for data analysis and modeling. In this paper, an automatic data mining tool, termed as ABCModeller (Automatic Binary Classification Modeller), with a user-friendly graphical interface was developed here, which includes automated functions as data preprocessing, significant feature extraction, classification modeling, model evaluation and prediction. In order to enhance the generalization ability of the final model, a consistent voting method was built here in this tool with the utilization of three popular machine-learning algorithms, as artificial neural network, support vector machine and random forest.
feature list: operation 3436
feature list: operation 3936
feature list: operation 3937
license: GPL-3.0

ABCNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0769
application sub category: topic 3361
citation: TPAMI.2021.3107437
citation: pubmed:34460364
description: Adaptive Bezier-Curve Network for Real-time End-to-end Text Spotting.
is accessible for free: true
license: BSD-2-Clause
software version: V.2

AbCPE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 2830
application sub category: topic 3400
application sub category: topic 3948
application sub category: topic 3966
citation: fbinf.2021.709951
citation: pmcid:PMC9581038
citation: pubmed:36303781
description: AbCPE web server implements a multi-label classification algorithm that predicts antibody class(es) for epitopes. This data driven machine learning based algorithm offers prediction of epitopes potentially recognised by an individual or multiple classes of antibodies viz. IgG, IgE, IgA and IgM (excluding IgD).
feature list: operation_0252
feature list: operation_0416
feature list: operation_0480
feature list: operation 3891
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

ABCpred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic_0121
application sub category: topic 3400
citation: prot.21078
citation: pubmed:16894596
description: Server to predict linear B cell epitope regions in an antigen sequence, using an artificial neural network. This server will assist in locating epitope regions that are useful in selecting synthetic vaccine candidates, disease diagonosis and also in allergy research.
feature list: operation 2479
feature list: operation 2575
operating system: Linux
operating system: Mac
operating system: Windows
software help: ABC help.html
primary contact: Gajendra P.S. Raghava

ABCpred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0091
application sub category: topic_0634
application sub category: topic 3047
application sub category: topic 3474
citation: s11030-021-10292-6
citation: pubmed:34609711
description: ABCpred is a webserver for the discovery of acetyl- and butyryl-cholinesterase inhibitors.
is accessible for free: true
primary contact: 0000-0003-1040-663X

ABCRpred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0078
application sub category: topic_0154
application sub category: topic 3168
application sub category: topic 3474
citation: https://doi.org/10.1101/2021.06.26.450028
description: Prediction of antibiotic resistant strains of bacteria from their beta-lactamases protein.
feature list: operation_0321
feature list: operation 3482
feature list: operation 3935
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

ABCstats
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3315
application sub category: topic 3407
citation: acs.analchem.2c00503
citation: pubmed:35657711
description: ABCstats is an R package for metabolomics data transformation. Adaptive Box-Cox (ABC) transformation improves the data normality for statistical analysis.
feature list: operation 3435
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

AbDesign
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0130
application sub category: topic_0196
application sub category: topic_0623
application sub category: topic_0736
application sub category: topic_0821
citation: PRO.3970
citation: pmcid:PMC7737780
citation: pubmed:33040418
description: The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes.
feature list: operation_0249
feature list: operation_0310
feature list: operation_0479
feature list: operation 2488

AbDesigner3D
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2814
application sub category: topic 2830
application sub category: topic 3297
citation: bty055
description: Integrated online application for identification of optimal immunizing peptides for antibody production using peptide-based strategy.
feature list: operation_0252
operating system: Linux
operating system: Mac
operating system: Windows
software help: how-to.html
primary contact: Trairak Pisitkun

AbDev
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0176
application sub category: topic 3306
application sub category: topic 3474
citation: ACS.MOLPHARMACEUT.4C00804
citation: pubmed:39606945
description: AbDev is a machine learning tool for predicting 12 biophysical properties of monoclonal antibodies using variable region sequences. It combines deep learning (DeepSP) with machine learning techniques and offers a web application interface for predictions.
feature list: operation 2476
feature list: operation 3436
feature list: operation 3454

AbDiver
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic 2830
application sub category: topic 3168
application sub category: topic 3374
citation: btac151
description: AbDiver is a tool to explore the natural antibody landscape to aid therapeutic design.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3431
software help: abdiverdocumentation
primary contact: Konrad Krawczyk

ABDpred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0209
application sub category: topic 3324
application sub category: topic 3343
application sub category: topic 3379
application sub category: topic 3474
citation: ijmr.ijmr 1832 22
citation: pmcid:PMC10954100
citation: pubmed:38345040
description: Prediction of active antimicrobial compounds using supervised machine learning techniques.
feature list: operation 3436
feature list: operation 3482
feature list: operation 3927
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

ABDS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic 2259
application sub category: topic 3277
application sub category: topic 3360
citation: S41598-024-78076-0
citation: V1
citation: pmcid:PMC11569126
citation: pubmed:39550430
description: ABDS is an R tool suite designed for analyzing biologically diverse samples, specifically addressing challenges with missing data imputation, signature gene detection, and differential pattern visualization. It provides tools for mechanistic imputation, group-wise testing, and heatmap visualization.
feature list: operation 3557
feature list: operation 3744
feature list: operation 3891

ABEEM Solver
type: SoftwareApplication
input: Small molecule structure
  type: FormalParameter
  additional type: data 1463
output: Atomic property
  type: FormalParameter
  additional type: data 1917
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2258
application sub category: topic 3332
citation: jcc.20344
citation: pubmed:16381078
description: Calculates partial atomic charges for small organic molecules, drug-like molecules.
feature list: operation 2480
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
provider: ELIXIR-CZ
software help: jcc.20344
software help: licence.htm
software help: manual.htm
software version: 1.0
primary contact: Radka Svobodová Vařeková

ABEILLE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web application
application sub category: topic_0121
application sub category: topic_0203
application sub category: topic_0634
application sub category: topic 3170
application sub category: topic 3474
citation: btac603
citation: pmcid:PMC9563686
citation: pubmed:36063052
description: ABEILLE (ABerrant Expression Identification empLoying machine LEarning from sequencing data) is a variational autoencoder (VAE) based method for the identification of AGEs from the analysis of RNA-seq data without the need of replicates or a control group.
feature list: operation 3435
feature list: operation 3454
feature list: operation 3659
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

AbEMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 2830
application sub category: topic 3382
citation: s41596-023-00826-7
citation: pmcid:PMC10898366
citation: pubmed:37188806
description: Web server for the prediction of antibody epitopes.
feature list: operation_0252
feature list: operation_0416
feature list: operation_0479
feature list: operation_0480
feature list: operation 3899
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

Aber-OWL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0089
application sub category: topic_0219
citation: S12859-015-0456-9
citation: pmcid:PMC4384359
citation: pubmed:25627673
description: Framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies.
feature list: operation 3559
operating system: Linux
operating system: Mac
operating system: Windows
software help: about
primary contact: Robert Hoehndorf

abi2link
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0625
description: abi2link is designed to create linkage files out of ABI genotype and phenotype files.
feature list: operation_0335

abi2xml
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0654
description: abi2xml is a command line utility to convert an abi trace file to an xml file. Abi trace files contain DNA sequence data and are e.g. produced by ABI PRISM TM 377 DNA sequencers.
feature list: operation_0335
operating system: Linux
operating system: Mac
operating system: Windows
software help: abi2xml.sourceforge.net
software version: 1.2

Abiotic
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Pipeline for chemical exposome integration and analysis with biotic data

abiview
type: SoftwareApplication
input: Sequence trace
  type: FormalParameter
  additional type: data_0924
output: Sequence trace image
  type: FormalParameter
  additional type: data 2168
output: Nucleic acid sequence record
  type: FormalParameter
  additional type: data 2887
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0092
citation: S0168-9525(00)02024-2
citation: CBO9781139151399
citation: CBO9781139151405
contributor: EMBOSS Contributors
contributor: UK BBSRC
contributor: UK MRC
contributor: Wellcome Trust
description: Display the trace in an ABI sequencer file.
feature list: operation_0337
feature list: operation_0564
funder: UK BBSRC
funder: UK MRC
funder: Wellcome Trust
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
provider: EMBOSS
software help: ch01s01.html
software help: pr02s04.html
software help: abiview.html
software version: r6

abiview WS (husar)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0092
description: This tool reads in an ABI sequence trace file and graphically displays the results.
feature list: operation_0337
operating system: Linux
operating system: Mac
operating system: Windows
software help: abiview.html
software version: 1

AbLang
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0080
application sub category: topic_0154
application sub category: topic 2830
citation: vbac046
citation: pmcid:PMC9710568
citation: pubmed:36699403
description: An antibody language model for completing antibody sequences.
feature list: operation_0337
feature list: operation_0368
feature list: operation_0480
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
operating system: Windows

ABLE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2269
application sub category: topic 3382
citation: s12021-022-09601-7
citation: pubmed:36008650
description: Automated Brain Lines Extraction Based on Laplacian Surface Collapse.
feature list: operation 3435
feature list: operation 3791
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

ABM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0602
application sub category: topic_0621
application sub category: topic 3500
citation: JOURNAL.PONE.0252881
citation: pmcid:PMC8191904
citation: pubmed:34111183
description: ABM (Anaerobic Biodegradation Model). A mechanistic model of methane emission from animal slurry with a focus on microbial groups.
feature list: operation_0417
feature list: operation 2426
feature list: operation 3633
operating system: Linux
operating system: Mac
operating system: Windows

ABM-TKI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 2259
application sub category: topic 2640
citation: https://doi.org/10.1186/1471-2105-13-218
citation: pmcid:PMC3487967
citation: pubmed:22935054
description: Employing agent-based model (ABM) tool to simulate brain tumor growth that includes an EGFR signaling pathway together with a related cell-cycle pathway, angiogenesis and tyrosine kinase inhibitors (TKIs) treatment. The users can apply this tool to predict the responses of brain cancer to TKIs, and to reveal the dual role of angiogenesis during TKI treatment.
feature list: operation 2426
feature list: operation 3660
operating system: Linux
operating system: Mac
operating system: Windows
software help: multi-scale1
primary contact: Xiaoqiang Sun

ABMapper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0097
application sub category: topic_0102
citation: btq656
citation: pmcid:PMC3031031
citation: pubmed:21169377
description: Portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping.
feature list: operation 2423
feature list: operation 2478
feature list: operation 2520
operating system: Linux
operating system: Mac
operating system: Windows
software help: abmapper
primary contact: Hong Kong Bioinformatics Center

abmR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0092
application sub category: topic_0610
application sub category: topic 3500
application sub category: topic 3679
citation: https://doi.org/10.1101/2021.09.15.460374
description: abmR is an R package for agent-based model analysis of large-scale movements across taxa. Agent-based modeling (ABM) shows promise for animal movement studies. However, a robust, open-source, and spatially explicit ABM coding platform is currently lacking. We present abmR, an R package for conducting continental-scale ABM simulations across animal taxa. The package features two movement functions, each of which relies on the Ornstein-Uhlenbeck (OU) model. The theoretical background for abmR is discussed and the main functionalities are illustrated using two example populations. Potential future additions to this open-source package may include the ability to specify multiple environmental variables or to model interactions between agents. Additionally, updates may offer opportunities for disease ecology and integration with other R movement modeling packages
feature list: operation_0337
feature list: operation 3946
software help: abmr

ABNER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3047
application sub category: topic 3070
citation: bti475
citation: pubmed:15860559
description: ABNER (A Biomedical Named Entity Recognizer) is a software tool for molecular biology text analysis.
feature list: operation_0306
operating system: Linux
operating system: Mac
operating system: Windows
software help: javadoc
software version: 1.5

Aboria
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0176
citation: j.softx.2017.07.002
description: Aboria is a powerful and flexible C++ library for the implementation of particle-based numerical methods. The particles in such methods can represent actual particles (e.g. Molecular Dynamics) or abstract particles used to discretise a continuous function over a domain (e.g. Radial Basis Functions).
feature list: operation 2476
license: BSD-3-Clause
operating system: Linux
software help: Aboria
software version: v0.4
primary contact: Martin Robinson

ABOSA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3303
citation: j.cmpb.2022.107120
citation: pubmed:36152624
description: Automatic blood oxygen saturation signal analysis software. This software automatically detects desaturation and following recovery events from the blood oxygen saturation signal. The software calculates numerous event-specific metrics for each scored event.
feature list: operation 2428
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

ABPEPserver
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0108
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 2830
citation: s12885-023-10970-8
citation: pmcid:PMC10239192
citation: pubmed:37270525
description: Web application for documentation and analysis of substitutants.
feature list: operation_0314
feature list: operation 2940
feature list: operation 3629
feature list: operation 3799
is accessible for free: true
license: MIT

abPOA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0769
citation: https://doi.org/10.1101/2020.05.07.083196
description: abPOA can perform multiple sequence alignment (MSA) on a set of input sequences and generate a consensus sequence by applying the heaviest bundling algorithm to the final alignment graph.
feature list: operation_0310
feature list: operation_0492
feature list: operation_0496
license: MIT

ABRA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0196
application sub category: topic 3168
citation: btu376
citation: pmcid:PMC4173014
citation: pubmed:24907369
description: Realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).
feature list: operation_0310
feature list: operation_0452
feature list: operation 3198
operating system: Linux
operating system: Mac
operating system: Windows
software help: abra

ABrainVis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3452
citation: S12938-021-00909-0
citation: pmcid:PMC8323223
citation: pubmed:34325693
description: Android brain image visualization tool.
feature list: operation_0337
is accessible for free: true
license: GPL-3.0

abriTAMR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3301
application sub category: topic 3305
application sub category: topic 3324
application sub category: topic 4013
description: an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.
feature list: operation 3482
software version: 1.0.14
software version: 1.0.3

ABS
type: SoftwareApplication
input: Gene name
  type: FormalParameter
  additional type: data 2299
input: Transcription factor identifier
  type: FormalParameter
  additional type: data 1077
input: ABS ID
  type: FormalParameter
  additional type: data 2741
output: Nucleic acid features
  type: FormalParameter
  additional type: data 1276
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0749
citation: gkj116
citation: pmcid:PMC1347478
citation: pubmed:16381947
description: Annotated regulatory binding sites from orthologous promoters.
feature list: operation_0224
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: Genome BioInformatics Research Lab
software help: docs.html

ABS-Scan
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0128
application sub category: topic 2275
citation: f1000research.5165.2
citation: pmcid:PMC4319546
citation: pubmed:25685322
description: Performs alanine scanning mutagenesis for a given protein-ligand complex.
feature list: operation_0239
feature list: operation 2423
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.php
primary contact: Nagasuma Chandra

AbSim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2830
application sub category: topic 3297
application sub category: topic 3524
citation: btx533
description: Simulation methods for the evolution of antibody repertoires. The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. Both single lineages using one set of V-, D-, and J-genes or full repertoires can be simulated.
feature list: operation_0477
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: AbSim.pdf
software version: 0.2.4
primary contact: Alexander Yermanos

AbsoluRATE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0634
application sub category: topic 3374
citation: J.BBAPAP.2021.140682
citation: pubmed:34102324
description: An in-silico method to predict the aggregation kinetics of native proteins.
feature list: operation 3431
feature list: operation 3436
feature list: operation 3659
operating system: Mac
operating system: Windows

Absolute and Comparison Analysis for Affymetrix Data
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic 3374
description: Perform single-array and comparison analysis for Affymetrix data given by CEL and CDF files.
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: Abram Jujunashvili

ABSP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0654
application sub category: topic 3168
application sub category: topic 3295
application sub category: topic 3519
application sub category: topic 3674
citation: btad008
citation: pmcid:PMC9846423
citation: pubmed:36629453
description: Automated R tool to efficiently analyse region-specific CpG methylation from bisulfite sequencing PCR.
feature list: operation 3185
feature list: operation 3186
feature list: operation 3206
feature list: operation 3207
feature list: operation 3919
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

ABSSeq
type: SoftwareApplication
input: Gene expression data
  type: FormalParameter
  additional type: data 2603
  encoding format: format 2032
output: Plot
  type: FormalParameter
  additional type: data 2884
  encoding format: format 3617
output: Mathematical model
  type: FormalParameter
  additional type: data_0950
  encoding format: format 2032
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
additional type: Plug-in
application sub category: topic_0203
application sub category: topic 2269
application sub category: topic 3170
citation: s12864-016-2848-2
citation: pmcid:PMC4973090
citation: pubmed:27488180
description: An R package which provides RNA-Seq analysis based on modelling absolute expression differences.
feature list: operation_0337
feature list: operation 2238
feature list: operation 2426
feature list: operation 2495
feature list: operation 3223
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ABSSeq.html
software version: 1.10.0
primary contact: Wentao Yang

abstcal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2640
application sub category: topic 3305
application sub category: topic 3379
citation: ntab083
citation: pmcid:PMC8826113
citation: pubmed:33912971
description: abstcal is a a Python package to calculate abstinence results using the timeline followback interview data.
feature list: operation 3436
feature list: operation 3557
license: MIT

ABySS
type: SoftwareApplication
input: DNA sequence (raw)
  type: FormalParameter
  additional type: data 3497
  encoding format: format 1929
  encoding format: format 1930
output: Sequence assembly
  type: FormalParameter
  additional type: data_0925
  encoding format: format 1929
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
author: Shaun Jackman
citation: gr.089532.108
citation: gr.214346.116
citation: pmcid:PMC2694472
citation: pmcid:PMC5411771
citation: pubmed:19251739
citation: pubmed:28232478
description: De novo genome sequence assembler using short reads.
feature list: operation_0524
feature list: operation_0525
feature list: operation 3216
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
provider: BC Cancer Agency Genome Sciences Centre
provider: bcgsc.ca
software help: abyss
software version: 1.0-2.3.7
primary contact: Shaun Jackman

AC-Caps
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 3295
application sub category: topic 3474
application sub category: topic 3534
citation: S12539-020-00379-3
citation: pubmed:32572768
description: AC-Caps is a deep learning method used for predicting the RBP binding sites on lncRNA chains.
feature list: operation_0253
feature list: operation_0303
feature list: operation 2575
feature list: operation 3927
operating system: Windows

AC-PCoA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3170
application sub category: topic 3305
application sub category: topic 3512
application sub category: topic 3673
application sub category: topic 3697
citation: journal.pcbi.1010184
citation: pmcid:PMC9278763
citation: pubmed:35830390
description: Adjustment for Confounding factors using Principal Coordinate Analysis (AC-PCoA) is a R package that adjust for confounding factors using principal coordinate analysis.
feature list: operation 2939
feature list: operation 3891
feature list: operation 3935
feature list: operation 3960
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

AC2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0078
application sub category: topic_0121
application sub category: topic 3474
citation: https://doi.org/10.3390/E23050530
citation: pmcid:PMC8146440
citation: pubmed:33925812
description: AC2 is an efficient protein sequence compression tool using artificial neural networks and cache-hash models.
feature list: operation_0267
feature list: operation 3927
license: GPL-3.0

ac4C-AFL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0091
application sub category: topic_0108
application sub category: topic_0203
application sub category: topic 3474
application sub category: topic 3512
citation: J.OMTN.2024.102192
citation: pmcid:PMC11108997
citation: pubmed:38779332
description: ac4C-AFL is a bioinformatics tool for high-precision identification of human mRNA N4-acetylcytidine (ac4C) sites based on adaptive feature representation learning. A web server is available at the provided URL.
feature list: operation_0314
feature list: operation 3092
feature list: operation 3937

ACA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3318
application sub category: topic 3382
citation: pmcid:PMC8299461
citation: pubmed:34308361
description: Adaptive Checkpoint Adjoint Method for Gradient Estimation in Neural ODE.
operating system: Linux
operating system: Mac
operating system: Windows

AcaFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0114
application sub category: topic_0160
application sub category: topic_0622
citation: msystems.00817-22
citation: pmcid:PMC9765179
citation: pubmed:36413017
description: Genome mining for anti-CRISPR associated genes.
feature list: operation_0435
feature list: operation_0477
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

Accel-Align
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0081
application sub category: topic_0102
application sub category: topic 3676
citation: https://doi.org/10.1101/2020.07.20.211888
description: A Fast Sequence Mapper and Aligner based on the Seed–Embed–Extend Method. Accel-Align does base-to-base alignment by default.
feature list: operation_0292
feature list: operation 3096
feature list: operation 3186
feature list: operation 3198
feature list: operation 3211

ACCoNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3382
citation: tcyb.2022.3162945
citation: pubmed:35417367
description: A adjacent context coordination network (ACCoNet) to explore the coordination of adjacent features in an encoder-decoder architecture for RSI-SOD.
license: Not licensed

Accucopy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0622
application sub category: topic 3673
application sub category: topic 3676
citation: https://doi.org/10.1101/2020.01.02.892364
description: Accucopy is a CNA-calling method that extends our previous Accurity model to predict both total (TCN) and allele-specific copy numbers (ASCN) for the tumor genome. Accucopy adopts a tiered Gaussian mixture model coupled with an innovative autocorrelation-guided EM algorithm to find the optimal solution quickly. The Accucopy model utilizes information from both total sequencing coverage and allelic sequencing coverage.
feature list: operation 3233
feature list: operation 3435

accuEnhancer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0749
application sub category: topic 2229
application sub category: topic 3168
application sub category: topic 3295
application sub category: topic 3474
citation: https://doi.org/10.1101/2020.11.10.375717
description: Accurate enhancer prediction by integration of multiple cell type data with deep learning. Enhancers are one class of the regulatory elements that have been shown to act as key components to assist promoters in modulating the gene expression in living cells. accuEnhancer utilize DNase data to build a deep learning model for predicting the H3K27ac peaks as the active enhancers in selected cell types. Moreover, we also tested joint training for multiple cell types to boost the model performance.
feature list: operation_0440
feature list: operation 2575
feature list: operation 3222

AccuVIR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic_0622
application sub category: topic 3673
citation: btac827
citation: pmcid:PMC9825286
citation: pubmed:36610711
description: AccuVIR -- an Accurate VIRal genome assembler and polisher -- utilizes path searching and sampling in sequence alignment graphs to assemble or polish draft assembly of viral genomes.
feature list: operation_0292
feature list: operation_0525
feature list: operation 3196
license: Not licensed

ACD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3370
application sub category: topic 3524
citation: s0021-9673(03)00393-5
citation: pubmed:12779216
description: Tool to search a knowledge base of the most commonly used chromatographic columns to locate those with the properties best-suited to the separation at hand. The Column Selector database contains information for 254 characterized columns, along with results for >4800 systematic experiments.
feature list: operation 2421
operating system: Linux
operating system: Mac
operating system: Windows
software help: colsel

ACDA
type: SoftwareApplication
input: Drug report
  type: FormalParameter
  additional type: data 1696
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0202
application sub category: topic 2640
application sub category: topic 3474
citation: vbad051
citation: pmcid:PMC10125903
citation: pubmed:37113249
description: Implementation of an augmented drug synergy prediction algorithm.
feature list: operation_0337
feature list: operation 3659
feature list: operation 4009
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: acda.readthedocs.io

acdc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3071
citation: S0168-9525(00)02024-2
citation: CBO9781139151399
citation: CBO9781139151405
contributor: EMBOSS Contributors
contributor: UK BBSRC
contributor: UK MRC
contributor: Wellcome Trust
description: Test an application ACD file.
feature list: operation_0336
funder: UK BBSRC
funder: UK MRC
funder: Wellcome Trust
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
provider: EMBOSS
software help: ch01s01.html
software help: pr02s04.html
software help: acdc.html
software version: r6

ACDC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 2229
application sub category: topic 3056
citation: btx054
citation: pmcid:PMC5447237
citation: pubmed:28158442
description: Automated cell type discovery and classification through knowledge transfer.
feature list: operation 3460
operating system: Mac
software help: acdc
primary contact: Brian Kidd
primary contact: Joel Dudley

acdc
type: SoftwareApplication
input: Sequence assembly
  type: FormalParameter
  additional type: data_0925
  encoding format: format 1929
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0091
author: Markus Lux
citation: s12859-016-1397-7
citation: pmcid:PMC5168860
citation: pubmed:27998267
description: A tool to test next-generation-sequencing (NGS) data from single-cell sequencing for contamination. By using sophisticated dimensionality reduction and clustering methods, it uses tetramer profiles to differentiate between different species in a given sample.
feature list: operation_0291
is accessible for free: true
license: MIT
operating system: Linux
software help: https://bibiserv.cebitec.uni-bielefeld.de/acdc
software version: 1.0
primary contact: Markus Lux

acde
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 3053
application sub category: topic 3308
citation: 978-0-387-49317-6 9
description: This package provides a multivariate inferential analysis method for detecting DE genes. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR).
feature list: operation 2495
feature list: operation 3658
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: acde.html
software version: 1.4.0
primary contact: Juan Pablo Acosta

acdpretty
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3071
citation: S0168-9525(00)02024-2
citation: CBO9781139151399
citation: CBO9781139151405
contributor: EMBOSS Contributors
contributor: UK BBSRC
contributor: UK MRC
contributor: Wellcome Trust
description: Correctly reformat an application ACD file.
feature list: operation_0335
funder: UK BBSRC
funder: UK MRC
funder: Wellcome Trust
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
provider: EMBOSS
software help: ch01s01.html
software help: pr02s04.html
software help: acdpretty.html
software version: r6

acdtable
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3071
citation: S0168-9525(00)02024-2
citation: CBO9781139151399
citation: CBO9781139151405
contributor: EMBOSS Contributors
contributor: UK BBSRC
contributor: UK MRC
contributor: Wellcome Trust
description: Generate an HTML table of parameters from an application ACD file.
feature list: operation 2422
funder: UK BBSRC
funder: UK MRC
funder: Wellcome Trust
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
provider: EMBOSS
software help: ch01s01.html
software help: pr02s04.html
software help: acdtable.html
software version: r6

ACDtool
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2269
description: Web-server for the generic analysis of large data sets of counts.
is accessible for free: true

acdtrace
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3071
citation: S0168-9525(00)02024-2
citation: CBO9781139151399
citation: CBO9781139151405
contributor: EMBOSS Contributors
contributor: UK BBSRC
contributor: UK MRC
contributor: Wellcome Trust
description: Trace processing of an application ACD file (for testing).
feature list: operation_0336
funder: UK BBSRC
funder: UK MRC
funder: Wellcome Trust
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
provider: EMBOSS
software help: ch01s01.html
software help: pr02s04.html
software help: acdtrace.html
software version: r6

acdvalid
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3071
citation: S0168-9525(00)02024-2
citation: CBO9781139151399
citation: CBO9781139151405
contributor: EMBOSS Contributors
contributor: UK BBSRC
contributor: UK MRC
contributor: Wellcome Trust
description: Validate an application ACD file.
feature list: operation_0336
funder: UK BBSRC
funder: UK MRC
funder: Wellcome Trust
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
provider: EMBOSS
software help: ch01s01.html
software help: pr02s04.html
software help: acdvalid.html
software version: r6

ACE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0654
application sub category: topic 3168
citation: btv332
citation: pubmed:26026137
description: Corrects substitution errors in an Illumina archive using a k-mer trie.
feature list: operation 3195
operating system: Linux
operating system: Mac
software help: ACE

ACE-Molecule
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3047
application sub category: topic 3314
application sub category: topic 3372
citation: https://doi.org/10.1063/5.0002959
citation: pubmed:32241122
description: Advanced Computational Engine for Molecule (ACE-Molecule) is a quantum chemistry package based on a real-space numerical grid.
license: GPL-3.0
software help: home

ACE2 Netlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0625
application sub category: topic_0659
application sub category: topic_0804
application sub category: topic 2885
application sub category: topic 3404
citation: https://doi.org/10.1101/2020.10.27.20220665
description: In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility.
feature list: operation 3196
feature list: operation 3226
feature list: operation 3227

ACE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3324
application sub category: topic 3930
citation: bbad495
citation: pmcid:PMC10768796
citation: pubmed:38180831
description: Optimizing Combinatorial Design of Pooled ELISpot Assays with an Epitope Similarity Model. ACE facilitates (1) generation of ELISpot configurations (peptide-pool assignments) using a deep learning approach to cluster similar peptides and (2) deconvolution of pool spot counts for identification of immunogenic peptides.
feature list: operation_0252
feature list: operation_0416
feature list: operation 3629
feature list: operation 3631
feature list: operation 3799
is accessible for free: true
license: Apache-2.0

AcE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0654
description: It aids gene prediction accuracy evaluation. It uses GFF format to make it easy to convert gene prediction results into an analyzable format. Novel features include isoform accuracy evaluation from either the annotated gene or gene prediction perspective or both at the same time. Masking of genomic sequence which has unknown features allows gene predictions in annotated regions to be analyzed in a genomic context.
feature list: operation 2423
feature list: operation 2454
operating system: Linux
operating system: Mac
operating system: Windows
software help: SCM
software version: 0.5

ACE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic 3170
application sub category: topic 3511
citation: s12859-017-1741-6
citation: pmcid:PMC5504734
citation: pubmed:28693417
description: Efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data.
feature list: operation 3482
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.html
primary contact: Dianhao Guo
primary contact: Jiapeng Luo

ACEapi
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0625
application sub category: topic 3063
application sub category: topic 3303
application sub category: topic 3379
application sub category: topic 3474
citation: ocab027
citation: pmcid:PMC8279796
citation: pubmed:33712854
description: ACEapi is the API for the the Advanced Cohort Engine for searching longitudinal patient records.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3436
license: MIT
primary contact: Alison Callahan

ACEGEN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 3047
application sub category: topic 3336
application sub category: topic 3474
citation: ACS.JCIM.4C00895
citation: pmcid:PMC11581341
citation: pubmed:39092857
description: ACEGEN is a toolkit for generative drug design built using TorchRL, streamlining reinforcement learning for molecular generation. It offers a comprehensive and tested approach, validated through benchmarking and applied in multiple drug discovery case studies, and is available under the MIT license.
feature list: operation_0310
feature list: operation_0337
feature list: operation 4009
license: MIT

ACEInhibPKPD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2259
application sub category: topic 3315
application sub category: topic 3374
description: PKPD model for ACE inhibition with benazapril or cilazapril; ducational drug dosing app for treatment of high blood pressure
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: Ashlee N. Ford Versypt

ACELA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic_0602
application sub category: topic 2815
application sub category: topic 3474
citation: 1471-2105-9-s11-s8
citation: pmcid:PMC2586757
citation: pubmed:19025694
description: Tool that aims to reduce the human effort required to produce a gold standard corpus of named entity (NE) annotations.
feature list: operation 2409
feature list: operation 3280
feature list: operation 3778
operating system: Linux
operating system: Mac
operating system: Windows
software help: acela
primary contact: Yoshimasa Tsuruoka

ACEP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0082
application sub category: topic_0154
application sub category: topic_0160
application sub category: topic 3400
application sub category: topic 3474
citation: S12864-020-06978-0
citation: pmcid:PMC7455913
citation: pubmed:32859150
description: ACEP is a deep learning model for high-throughput antibacterial peptide recognition. By loading a pre-trained model, the software can be deployed on a common computer to perform antimicrobial peptide recognition, important motif discovery, and visualization analysis. Both the peptide sequences and PSSM profiles need to be input the model.
feature list: operation_0239
feature list: operation_0267
feature list: operation_0303
feature list: operation_0337
feature list: operation 3482

AceParser
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
description: AceParser: Parse an Ace file (Phred/Phrap output) into a tab-delimited assembly alignment file. Options to include embedded annotation from multiple sources.
feature list: operation_0226
feature list: operation_0310
feature list: operation_0335
feature list: operation 2928
operating system: Windows
software help: SoftwareC.html
software version: 1.33

ACES
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0196
application sub category: topic_0769
application sub category: topic 3168
application sub category: topic 3293
application sub category: topic 3512
citation: https://doi.org/10.1101/2021.06.16.448733
description: ACES (Analysis of Conservation with Expansive Species). Generates BLAST hits against each of the reference genomes, a multiple sequence alignment file, a graphical fragment assembly file, and a phylogenetic tree file.
feature list: operation_0224
feature list: operation_0323
feature list: operation_0492
feature list: operation_0552
feature list: operation_0567
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

AceView genes database
type: SoftwareApplication
input: Species name
  type: FormalParameter
  additional type: data 1045
input: Gene symbol
  type: FormalParameter
  additional type: data 1026
input: Species name
  type: FormalParameter
  additional type: data 1045
input: Species name
  type: FormalParameter
  additional type: data 1045
input: Gene ID (NCBI)
  type: FormalParameter
  additional type: data 1027
input: Species name
  type: FormalParameter
  additional type: data 1045
input: GenBank accession
  type: FormalParameter
  additional type: data 2292
input: Gene symbol
  type: FormalParameter
  additional type: data 1026
input: Gene symbol
  type: FormalParameter
  additional type: data 1026
input: Species name
  type: FormalParameter
  additional type: data 1045
input: Species name
  type: FormalParameter
  additional type: data 1045
input: Species name
  type: FormalParameter
  additional type: data 1045
input: Clone ID (IMAGE)
  type: FormalParameter
  additional type: data 2704
input: Gene symbol
  type: FormalParameter
  additional type: data 1026
input: Gene symbol
  type: FormalParameter
  additional type: data 1026
input: Species name
  type: FormalParameter
  additional type: data 1045
input: Species name
  type: FormalParameter
  additional type: data 1045
input: Clone ID (RefSeq)
  type: FormalParameter
  additional type: data 2803
output: Gene report
  type: FormalParameter
  additional type: data_0916
  encoding format: format 2331
output: Gene report
  type: FormalParameter
  additional type: data_0916
  encoding format: format 2331
output: Gene transcript report
  type: FormalParameter
  additional type: data 3134
  encoding format: format 2331
output: Gene report
  type: FormalParameter
  additional type: data_0916
  encoding format: format 2331
output: Nucleic acid features
  type: FormalParameter
  additional type: data 1276
  encoding format: format 2331
output: Nucleic acid features
  type: FormalParameter
  additional type: data 1276
  encoding format: format 2331
output: Gene report
  type: FormalParameter
  additional type: data_0916
  encoding format: format 2331
output: Gene report
  type: FormalParameter
  additional type: data_0916
  encoding format: format 2331
output: Gene report
  type: FormalParameter
  additional type: data_0916
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0623
application sub category: topic 3512
citation: j.immuni.2009.10.008
citation: pmcid:PMC3272079
citation: pubmed:20064451
description: A curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace).
feature list: operation_0224
operating system: Linux
operating system: Mac
operating system: Windows
provider: NCBI
software help: FAQ

ACG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0157
application sub category: topic 3056
citation: https://doi.org/10.1186/1471-2105-14-40
citation: pmcid:PMC3575405
citation: pubmed:23379678
description: The Ancestral Recombination Graph tool is a graphical desktop application that allows genetics researchers to infer properties of a population based on genetic sequences sampled from it.
feature list: operation 2478
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial.html
primary contact: Brendan O'Fallon

aCGH
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0622
application sub category: topic 3175
application sub category: topic 3518
citation: bti677
citation: pubmed:16159913
description: This tool includes functions for reading aCGH data from image analysis output files and clone information files or creating S3 objects for storing these data. It also incudes basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.
feature list: operation 3443
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: aCGH.html
software version: 1.52.0
primary contact: Peter Dimitrov

aCharges
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0082
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0166
citation: GKAD349
citation: pmcid:PMC10320090
citation: pubmed:37158246
description: Application for fast calculation of partial atomic charges of structures from the Alphafold database.
feature list: operation_0474
feature list: operation_0478
feature list: operation 3431
feature list: operation 3893
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

ACID
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic 3512
application sub category: topic 3518
citation: bth089
citation: pubmed:14962935
description: The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly.
feature list: operation_0310
feature list: operation_0525
feature list: operation_0527
feature list: operation 2478
feature list: operation 3432

Acidbio
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Suite
application sub category: topic_0769
citation: BTAC327
citation: pmcid:PMC9237710
citation: pubmed:35575355
description: Acidbio a system for automated testing and certification of bioinformatics file format interoperability.
feature list: operation_0335
feature list: operation_0336
feature list: operation 1812
feature list: operation 3216
feature list: operation 3431
is accessible for free: true
license: GPL-2.0

Acinetobase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 3071
application sub category: topic 3300
application sub category: topic 3382
citation: BAAC099
citation: pubmed:36412325
description: A database and repository of Acinetobacter strains
feature list: operation 2422
feature list: operation 3196
feature list: operation 3431
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

ACL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3384
application sub category: topic 3452
citation: j.bspc.2022.104486
citation: pmcid:PMC9721288
citation: pubmed:36505089
description: A framework for adjusting the threshold parameters according to the image contrast. Three functions include Attention mechanism threshold, Contour equalization, and Lung segmentation (ACL).
feature list: operation 3435
feature list: operation 3443
license: Not licensed

ACLAME
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0621
application sub category: topic_0623
application sub category: topic_0798
application sub category: topic 3053
application sub category: topic 3957
citation: gkp938
citation: pmcid:PMC2808911
citation: pubmed:19933762
description: This database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). In addition to providing information on the MGEs content, classifications are available at various levels of organization.
feature list: operation_0224
feature list: operation 2995
feature list: operation 3197
operating system: Linux
operating system: Mac
operating system: Windows
software help: description.html
primary contact: The ACLAME team

ACME
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0160
application sub category: topic_0654
application sub category: topic 3518
application sub category: topic 3656
citation: S0076-6879(06)11014-9
citation: pubmed:16939795
description: Set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is fast and can be applied on whole-genome tiling array experiments easily with enough memory.
feature list: operation 3501
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ACME.html
software version: 2.30.0
primary contact: http://orcid.org/0000-0002-8991-6458

aCMs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0097
application sub category: topic 2275
citation: s12859-015-0569-1
citation: pmcid:PMC4504443
citation: pubmed:26017195
description: The Ambivalent Covariance Models are stochastic homology search tools that support more than one consensus secondary RNA structures.
feature list: operation_0475
operating system: Linux
operating system: Mac
operating system: Windows
software help: http://bibiserv2.cebitec.uni-bielefeld.de/acms

ACNPD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0202
application sub category: topic_0602
application sub category: topic_0780
application sub category: topic 2640
citation: FPHAR.2021.746067
citation: pmcid:PMC8419280
citation: pubmed:34497528
description: The Database for Elucidating the Relationships Between Natural Products, Compounds, Molecular Mechanisms, and Cancer Types. ACNPD is an online tool that provides users with a quick search of the pharmacological mechanisms of natural anti-cancer products. The database contains 10 common cancer types, XXX compounds, XXX pharmacological mechanisms, involving PI3K/Akt, PI3K/Akt/mTOR, Wnt/ β-catenin and other signaling pathways. The web interface allows users to query related queries in a variety of ways.
feature list: operation_0306
feature list: operation 2421

ACO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0654
application sub category: topic 3474
application sub category: topic 3673
citation: V1
description: ACO is a lossless quality scores compression algorithm based on adaptive coding order and this software can be used for both encoding and decoding.
feature list: operation 1812
feature list: operation 3435
feature list: operation 3802
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Niu Yi

acorde
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Workflow
application sub category: topic_0102
application sub category: topic 2259
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3320
citation: s41467-022-29497-w
citation: pmcid:PMC8983708
citation: pubmed:35383181
description: A tool for isoform co-usage networks from single-cell RNA-seq data
feature list: operation_0264
feature list: operation_0313
feature list: operation 3463
feature list: operation 3799
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

ACORN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 3301
application sub category: topic 3324
application sub category: topic 3384
application sub category: topic 3418
citation: WELLCOMEOPENRES.18317.1
description: Clinically Oriented antimicrobial Resistance surveillance Network (ACORN) as a lightweight but comprehensive platform, in which we combine clinical data collection with diagnostic stewardship, microbiological data collection and visualisation of the linked clinical-microbiology dataset.
feature list: operation_0337
feature list: operation 3482
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows

Acoustilytix
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3336
application sub category: topic 3373
application sub category: topic 3419
application sub category: topic 3474
citation: BRAINSCI11070864
citation: pmcid:PMC8301917
citation: pubmed:34209754
description: A Web-Based Automated Ultrasonic Vocalization Scoring Platform.
feature list: operation 2422

ACovPepDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0091
application sub category: topic_0154
application sub category: topic 3068
application sub category: topic 3071
citation: S41597-022-01394-3
citation: pmcid:PMC9192597
citation: pubmed:35697698
description: ACovPepDB is a comprehensive peptides database of anti-coronavirus peptides, which contains 518 enrties with 214 unique ACovPs manually extracted from research articles and public databases.
feature list: operation_0306
feature list: operation 2421
feature list: operation 3431
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows

ACP-CapsPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 2640
application sub category: topic 3336
application sub category: topic 3474
citation: BBAE460
citation: pmcid:PMC11410379
citation: pubmed:39293807
description: ACP-CapsPred is a computational framework using capsule networks to identify anticancer peptides and predict their functional activities across different cancer types. The tool integrates protein language models, evolutionary information, and physicochemical properties to expedite ACP development.
feature list: operation 3631
feature list: operation 3891
feature list: operation 3927

ACP-DA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 3315
application sub category: topic 3474
citation: FGENE.2021.698477
citation: pmcid:PMC8279753
citation: pubmed:34276801
description: Improving the Prediction of Anticancer Peptides Using Data Augmentation.
feature list: operation 3435
feature list: operation 3935
operating system: Linux
operating system: Mac
operating system: Windows

ACP-MHCNN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3474
citation: https://doi.org/10.1101/2020.09.25.313668
description: An Accurate Multi-Headed Deep-Convolutional Neural Network to Predict Anticancer peptides.
feature list: operation 3631
feature list: operation 3927
feature list: operation 3937

ACP-MLC
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
output: Score
  type: FormalParameter
  additional type: data 1772
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 3474
citation: j.compbiomed.2023.106844
citation: pubmed:37058760
description: A two-level prediction engine for identification of anticancer peptides and multi-label classification of their functional types.
feature list: operation 3631
feature list: operation 3936
is accessible for free: true
operating system: Windows
software help: Manual.pdf

ACP_MS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2640
citation: bbac462
citation: pubmed:36326080
description: A prediction model of anticancer peptides based on feature extraction.
feature list: operation 3631
feature list: operation 3937
is accessible for free: true

ACPred-BMF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 3474
citation: s41598-022-24404-1
citation: pmcid:PMC9763336
citation: pubmed:36535969
description: ACPred-BMF server is used for anticancer peptide (ACP) prediction.
feature list: operation_0267
feature list: operation 3631
feature list: operation 3891
feature list: operation 3935
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

ACPred-LAF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 3474
citation: BTAB560
citation: pubmed:34323948
description: Learning embedding features based on multi-sense-scaled attention architecture to improve the predictive performance of anticancer peptides.
feature list: operation 3435
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

ACPredStackL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 2640
application sub category: topic 3379
application sub category: topic 3474
citation: bbaa312
citation: pmcid:PMC8294543
citation: pubmed:33316035
description: ACPredStackL is a ensemble learning framework using stacking strategy for accurate identification of ACPs. Anticancer peptides (ACPs),known as potential future therapeutics for cancer, have been studied extensively,attribution to their unique ability to target cancer cells without affecting healthy cells directly.Many peptide-based drugs are currently being evaluated in preclinical and clinical trial.
feature list: operation 3631
feature list: operation 3900
feature list: operation 3936

ACPYPE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0593
application sub category: topic 1317
citation: https://doi.org/10.1186/1756-0500-5-367
citation: pmcid:PMC3461484
citation: pubmed:22824207
description: A tool based on Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN tools or ARIA.
feature list: operation 2480
is accessible for free: true
operating system: Linux
operating system: Mac
provider: Instruct
software help: wikis
software version: 1

ACPYPE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0077
application sub category: topic_0154
application sub category: topic_0176
application sub category: topic 3047
application sub category: topic 3306
citation: btad350
citation: pmcid:PMC10264366
citation: pubmed:37252824
description: The ACPYPE web server for small-molecule MD topology generation.
feature list: operation_0337
feature list: operation 2476
feature list: operation 3893
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

AcrDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0114
application sub category: topic_0621
application sub category: topic_0637
application sub category: topic_0749
application sub category: topic 3912
citation: GKAA857
citation: pubmed:33068435
description: AcrDB is a database of computationally predicted anti-CRISPR (Acr) and Acr-associated (Aca) operon database. Acr (anti-CRISPR) proteins are short proteins usually found in phages prophages and other mobile genetic elements that can turn off the CRISPR-Cas system of their prokaryotic hosts.
feature list: operation_0435
feature list: operation_0579
feature list: operation 3096
license: GPL-3.0

AcrDetector
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0622
application sub category: topic_0749
application sub category: topic 2269
author: Chuand Dong
citation: https://doi.org/10.1101/2020.05.23.112011
description: A tool to determine anti-CRISPR proteins in the whole genome-scale
provider: Chuand Dong

Absolute concentration robustness explorer (ACRE)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0602
application sub category: topic_0821
application sub category: topic 3895
citation: YSX001
citation: pmcid:PMC7513739
citation: pubmed:32995502
description: Absolute concentration robustness explorer (ACRE) explores combinatorial biochemical networks for the Absolute concentration robustness property.
feature list: operation 1812
feature list: operation 3927
license: Apache-2.0

AcrFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0091
application sub category: topic_0114
application sub category: topic_0121
application sub category: topic_0622
application sub category: topic_0769
citation: GKAA351
citation: pmcid:PMC7319584
citation: pubmed:32402073
description: AcrFinder is a tool used to identify Anti-CRISPR proteins (Acr) using both sequence homology and guilt-by-association approaches.
feature list: operation_0435
feature list: operation_0579
feature list: operation 1812
feature list: operation 2421
license: GPL-3.0

AcrHub
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0102
application sub category: topic_0160
application sub category: topic_0798
application sub category: topic 2814
application sub category: topic 3293
citation: GKAA951
citation: pubmed:33137193
description: AcrHub is an integrative database to provide an all-in-one user-friendly solution for anti-CRISPR proteins (Acr) investigation, prediction, mapping and relationship analysis. Bacteria and archaea have developed a wide variety of CRISPR-Cas systems to protect themselves from harmful mobile genetic elements (MGEs), such as phages and plasmids.
feature list: operation_0267
feature list: operation_0324
feature list: operation 3096
software help: help.jsp

AcrNET
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
output: Score
  type: FormalParameter
  additional type: data 1772
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0160
application sub category: topic 2275
application sub category: topic 3293
application sub category: topic 3474
citation: btad259
citation: pmcid:PMC10174705
citation: pubmed:37084259
description: Predicting anti-CRISPR with deep learning.
feature list: operation_0272
feature list: operation 1777
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

ACSNI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 3047
application sub category: topic 3474
citation: J.PATTER.2021.100270
citation: pmcid:PMC8212143
citation: pubmed:34179848
description: An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profiles.
feature list: operation_0314
feature list: operation_0533
feature list: operation 2436
feature list: operation 3927
feature list: operation 3935
operating system: Linux
operating system: Mac
operating system: Windows

Arabidopsis Co-expression Tool (ACT)
type: SoftwareApplication
input: Gene identifier
  type: FormalParameter
  additional type: data 1025
output: Gene tree
  type: FormalParameter
  additional type: data 3271
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3308
citation: j.isci.2021.102848
citation: j.xpro.2022.101208
citation: gkl204
citation: j.1365-313x.2006.02681.x
citation: biology11071019
citation: genes16030258
citation: pmcid:PMC11942487
citation: pmcid:PMC1538833
citation: pmcid:PMC8334378
citation: pmcid:PMC8885756
citation: pmcid:PMC9312353
citation: pubmed:16623895
citation: pubmed:16845059
citation: pubmed:34381973
citation: pubmed:35243384
citation: pubmed:36101400
citation: pubmed:40149410
description: The Arabidopsis Coexpression Tool (ACT) is based on the coexpression analysis of 21273 Arabidopsis thaliana genes from gene pair correlation data of 3500 Affymetrix Arabidopsis ATH1 Genome Array Chip microarray samples.
feature list: operation 2938
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
software version: 2.6
primary contact: https://orcid.org/0000-0001-8991-8712
primary contact: https://orcid.org/0000-0002-0519-3820

ACTION
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3475
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3308
citation: s41467-018-03933-2
citation: pmcid:PMC5904143
citation: pubmed:29666373
description: A method for inferring the functional identity of cells from their transcriptional profile, classifying them based on their dominant function, and reconstructing regulatory networks that are responsible for mediating their identity.
feature list: operation 1781
feature list: operation 3439
is accessible for free: true
license: Freeware
software help: ACTION
primary contact: Shahin Mohammadi

ACTIVA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0099
application sub category: topic 3170
application sub category: topic 3474
citation: https://doi.org/10.1101/2021.01.28.428725
description: ACTIVA is a realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders.
feature list: operation_0314
feature list: operation 3799
license: MIT

ActiveDriverDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0199
application sub category: topic_0601
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3922
citation: FCELL.2021.626821
citation: pmcid:PMC8021862
citation: pubmed:33834021
description: Interpreting Genetic Variation in Human and Cancer Genomes Using Post-translational Modification Sites and Signaling Networks (2021 Update). Find your mutation or gene of interest. You are viewing an updated version (2021) of the ActiveDriverDB. To view the previous version please visit activedriverdb.org/v2020. cystic fibrosis mutations in CFTR. ActiveDriverDB is a human proteo-genomics database. cancer mutations in CTNNB1 phosphodegron.
feature list: operation_0417
feature list: operation 3196
feature list: operation 3226
feature list: operation 3227
feature list: operation 3755
software help: tutorial
primary contact: Jüri Reimand
primary contact: Michał Krassowski

activeTF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0203
application sub category: topic_0749
citation: j.ygeno.2009.12.006
citation: pubmed:20060041
description: This tool finds a set of coordinately activated Transcription Factors (TF) from a given gene expression dataset.
feature list: operation_0445
operating system: Linux
operating system: Mac
operating system: Windows
software help: hulab.ucf.edu
primary contact: Harris Engineering Center

ACValidator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic_0659
application sub category: topic 3170
application sub category: topic 3512
citation: BPAA010
citation: pmcid:PMC7415914
citation: pubmed:32793805
description: Assembly based Circular RNA validator (ACValidator) is a bioinformatics approach to perform in silico validation of selected circular RNA junction(s).
feature list: operation_0308
feature list: operation_0310
feature list: operation 2428
feature list: operation 3454
license: MIT

AD-AE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0203
application sub category: topic 3474
citation: BTAA796
citation: pmcid:PMC7773484
citation: pubmed:33381842
description: Adversarial Deconfounding AutoEncoder (AD-AE) is a tool to deconfounding gene expression latent spaces.
feature list: operation_0314
feature list: operation 3435
feature list: operation 3935

AD-ENM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic_0176
application sub category: topic_0602
application sub category: topic_0611
application sub category: topic 3382
citation: j.jmb.2004.12.020
citation: j.str.2005.01.017
citation: pnas.2235686100
citation: biophysj.105.063305
citation: pmcid:PMC1366515
citation: pmcid:PMC263771
citation: pubmed:14585932
citation: pubmed:15713460
citation: pubmed:15837195
citation: pubmed:15879477
description: Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.
feature list: operation_0244
feature list: operation_0474
feature list: operation_0477
feature list: operation 3660
operating system: Linux
operating system: Mac
operating system: Windows
software help: jcp security.xml
primary contact: Wenjun Zheng

Alzheimer disease identification and classification
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0634
application sub category: topic_0637
application sub category: topic 3344
description: MATLAB script for Alzheimer disease identification and classification
feature list: operation 3443
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0
primary contact: Matlab Mebin

AD Knowledge Portal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
additional type: Web API
application sub category: topic_0634
application sub category: topic 3170
application sub category: topic 3277
application sub category: topic 3308
application sub category: topic 3489
citation: CPHG.105
citation: pmcid:PMC7587039
citation: pubmed:33085189
description: The AD Knowledge Portal (adknowledgeportal.org) is a public data repository that shares data and other resources generated by multiple collaborative research programs focused on aging, dementia, and Alzheimer's disease (AD).
feature list: operation_0224
feature list: operation 3435

ADA-M
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3337
application sub category: topic 3571
citation: S41525-018-0057-4
citation: pmcid:PMC6056554
citation: pubmed:30062047
description: Responsible sharing of biomedical data and biospecimens via the "Automatable Discovery and Access Matrix" (ADA-M). The Automatable Discovery and Access Matrix (ADA-M) provides a standardized way to unambiguously represent the conditions related to data discovery and access. By adopting ADA-M, data custodians can generally describe what their data are (the Header section), who can access them (the Permissions section), terms related to their use (the Terms section), and special conditions (the Meta-Conditions). By doing so, data custodians can participate in data sharing and collaboration by making meta information about their data computer-readable and hence directly available for digital communication, searching and automation activities.
feature list: operation 2421
feature list: operation 3435
license: Apache-2.0

adabmDCA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0099
application sub category: topic 2269
application sub category: topic 3474
citation: S12859-021-04441-9
citation: pmcid:PMC8555268
citation: pubmed:34715775
description: Adaptive Boltzmann machine learning for Potts models of biological data (adabmDCA) This is an implementation of the Boltzmann machine learning to infer several maximum-entropy statistical models of Potts or Ising variables given a set of observables. More precisely, it infers the couplings and the fields of a set of generalized Direct Coupling Analysis (DCA) models given a Multiple Sequence Alignment (MSA) of protein or RNA sequences. It is also possible to infer an Ising model from a set of spin configurations. The learning is performed via a gradient ascent of the likelihood of the data in which the model observables are computed via a Markov Chain Monte Carlo (MCMC) sampling.
feature list: operation_0272
feature list: operation_0477
feature list: operation 2939
feature list: operation 3658
feature list: operation 3891
is accessible for free: true
license: MIT
software help: documentation.md
primary contact: https://orcid.org/0000-0003-3937-3763

ADaCGH2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3175
citation: btu099
citation: pubmed:24532724
description: Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.
feature list: operation 3233
license: GPL-3.0
operating system: Mac
operating system: Windows
software help: ADaCGH2.html
software version: 2.14.0
primary contact: http://orcid.org/0000-0002-6637-9039

ADACT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic_0091
application sub category: topic_0203
application sub category: topic 3293
citation: BTAA853
citation: pubmed:33016997
description: A Tool for Analysing (Dis)similarity among Nucleotide and Protein Sequences Using Minimal and Relative Absent Words. ADACT (The Alignment-free Dissimilarity Analysis & Comparison Tool) measures dissimilarities among several species in an alignment-free manner. ADACT takes several genome sequences and some parameters (e.g. K-mer size, absent word type, dissimilarity index, RC-setting) as input, and outputs distance matrix, sorted species relationship and phylogenetic trees (neighbor joining tree and UPGMA tree) among species.
feature list: operation_0289
feature list: operation_0325
feature list: operation_0544
feature list: operation 3096
software help: wiki

AdaLiftOver
type: SoftwareApplication
input: Pair sequence alignment
  type: FormalParameter
  additional type: data 1381
  encoding format: format 3982
output: Sequence similarity score
  type: FormalParameter
  additional type: data_0865
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0621
application sub category: topic 2885
application sub category: topic 3168
application sub category: topic 3173
application sub category: topic 3517
citation: btad149
citation: pmcid:PMC10085516
citation: pubmed:37004197
description: High-resolution identification of orthologous regulatory elements with Adaptive liftOver.
feature list: operation_0224
feature list: operation 2429
feature list: operation 3659
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

ADAM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3524
citation: j.livsci.2008.06.028
description: Model selective breeding schemes for animals using stochastic simulation. The program simulates a population of animals and traces the genetic changes in the population under different selective breeding scenarios. It caters for different population structures, genetic models, selection strategies, and mating designs. It can be used to evaluate breeding schemes and generate genetic data to test statistical tools.
feature list: operation 2426
license: Not licensed
operating system: Linux
software help: manual website.htm

Adamant
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0769
application sub category: topic 3382
application sub category: topic 3489
application sub category: topic 3520
citation: F1000RESEARCH.110875.2
citation: pmcid:PMC9178528
citation: pubmed:35707001
description: Adamant is a JSON schema-based metadata creation tool for various research data management workflows.
feature list: operation 2422
feature list: operation 3435
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

ADAP-KDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
application sub category: topic_0769
application sub category: topic 3172
application sub category: topic 3370
application sub category: topic 3520
citation: ACS.ANALCHEM.1C00355
citation: pubmed:34455770
description: A Spectral Knowledgebase for Tracking and Prioritizing Unknown GC-MS Spectra in the NIH's Metabolomics Data Repository.
feature list: operation 3215
feature list: operation 3627
feature list: operation 3801
feature list: operation 3860
operating system: Linux
operating system: Mac
operating system: Windows

AdaPPI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0108
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic 3474
application sub category: topic 3957
citation: bbac523
citation: pubmed:36526282
description: iIentification of novel protein functional modules via adaptive graph convolution networks in a protein-protein interaction network.
feature list: operation_0276
feature list: operation 3094
feature list: operation 3660
feature list: operation 4009
is accessible for free: true
license: MIT

ADAPT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0659
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3837
citation: BTAE661
citation: pmcid:PMC11959182
citation: pubmed:39509330
description: ADAPT is an R package for differential abundance analysis of microbiome metagenomics data, using Tobit models to account for zero counts and an innovative method to identify differentially abundant taxa. It is available on Bioconductor and Github and comes with extensive documentation and installation options.
feature list: operation 2495
feature list: operation 3435
license: MIT

ADAPTER REMOVAL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0769
citation: bts311
citation: pmcid:PMC3400958
citation: pubmed:22628521
description: Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format.
feature list: operation 3237
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Vincent Moulton

AdapterRemoval
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.
feature list: operation_0232
feature list: operation 3192
feature list: operation 3237
software version: v2.3.2

adaptest
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 3053
application sub category: topic 3168
application sub category: topic 3518
description: Data-adaptive test statistics represent a general methodology for performing multiple hypothesis testing on effects sizes while maintaining honest statistical inference when operating in high-dimensional settings (). The utilities provided here extend the use of this general methodology to many common data analytic challenges that arise in modern computational and genomic biology.
feature list: operation 2424
feature list: operation 3223
feature list: operation 3659
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: adaptest.pdf
software version: 1.0.0
primary contact: Weixin Cai

Adaptivesplit
type: SoftwareApplication
input: Data
  type: FormalParameter
  additional type: data_0006
  encoding format: format 3752
output: Data
  type: FormalParameter
  additional type: data_0006
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3474
citation: https://doi.org/10.1101/2023.12.01.569626
contributor: Balint Kincses
contributor: Jialin Li
contributor: Raviteja Kotikalapudi
contributor: Robert Englert
contributor: Ulrike Bingel
description: External validation of machine learning models with adaptive sample splitting
feature list: operation 3359
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: adaptivesplit
software version: 0.1.0
primary contact: Tamas Spisak

AdaptML
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0080
application sub category: topic 3293
citation: science.1157890
citation: pubmed:18497299
description: Software package that will automatically partition groups of gene sequences according to both their genetic and ecological similarity.
feature list: operation 3478
operating system: Linux
operating system: Mac
operating system: Windows
software help: adaptml.html
primary contact: Eric Alm

ADAS-viewer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3295
application sub category: topic 3320
application sub category: topic 3334
application sub category: topic 3512
citation: S41540-021-00177-7
citation: pmcid:PMC7979890
citation: pubmed:33741983
description: ADAS-viewer (Visualization of Alzheimer's Disease Alternative Splicing) is a web-based application for integrative analysis of multi-omics data in Alzheimer's disease.
feature list: operation_0264
feature list: operation_0337
feature list: operation 3196
software help: Data.pdf
software help: Manual.pdf

ADASTRA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0203
application sub category: topic 2885
application sub category: topic 3125
citation: s41467-021-23007-0
citation: pmcid:PMC8115691
citation: pubmed:33980847
description: The database of Allelic Dosage-corrected Allele-Specific human Transcription factor binding sites provides a genomic map of allele-specific binding at hundreds thousands single-nucleotide polymorphisms constructed by meta-analysis of thousands of ChIP-Seq experiments.
feature list: operation 2409
is accessible for free: true
software help: help
software version: 5.1.2

ADAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0092
application sub category: topic_0121
application sub category: topic 3071
citation: jors.166
citation: pmcid:PMC6017986
citation: pubmed:29951204
description: Web Tool for Navigating and Plotting SomaLogic ADAT Files.
feature list: operation 2495
feature list: operation 2939
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: adat
primary contact: Foo Cheung

ADataViewer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3360
application sub category: topic 3379
application sub category: topic 3444
application sub category: topic 3452
citation: TRC2.12102
citation: pmcid:PMC7744022
citation: pubmed:33344750
description: ADataViewer is an interactive web application for identify cohort data sets that are suitable for their research in regards to the Alzheimer's disease data landscape.
feature list: operation_0337
feature list: operation 3196
feature list: operation 3435

AdaTiSS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 3068
application sub category: topic 3170
application sub category: topic 3518
citation: btab460
citation: pmcid:PMC8652109
citation: pubmed:34146104
description: A Novel Data-Adaptive Robust Method for Identifying Tissue Specificity Scores.
feature list: operation_0314
feature list: operation_0315
feature list: operation 3659
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

ADC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 2830
application sub category: topic 3170
citation: JOURNAL.PCBI.1009548
citation: pmcid:PMC8604336
citation: pubmed:34752449
description: ADC is an efficient method to identify highly interrelated genes across datasets.
feature list: operation 3223
feature list: operation 3435
feature list: operation 3891
primary contact: https://orcid.org/0000-0003-0192-7118

ADCdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 2830
application sub category: topic 3336
application sub category: topic 3379
citation: gkad831
citation: pmcid:PMC10768060
citation: pubmed:37831118
description: ADCdb: The database of antibody-drug conjugates.
feature list: operation_0224
feature list: operation_0480
feature list: operation 2421
is accessible for free: true
license: CC-BY-NC-4.0
operating system: Linux
operating system: Mac
operating system: Windows

addFeatures
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3245
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3245
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3382
description: addFeatures adds spot images to a Bruker SCiLS Lab mass spectrometry imaging dataset from a list of defined mass spectral features (m/z regions)
feature list: operation_0337
license: MIT
operating system: Windows
software help: addFeatures

Addgene
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0202
application sub category: topic 3047
application sub category: topic 3292
application sub category: topic 3336
application sub category: topic 3369
application sub category: topic 3376
citation: nbt.2177
citation: pubmed:22491276
description: Addgene is an nonprofit online database for plasmids and plasmid associated information.

AddictedChem
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 2840
application sub category: topic 3336
application sub category: topic 3474
citation: molecules27123931
citation: pmcid:PMC9227411
citation: pubmed:35745053
description: AddictedChem is a base of controlled substances and a platform for predicting NPS.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3216
feature list: operation 3929
feature list: operation 3938
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: help

AddictGene
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0102
application sub category: topic_0128
application sub category: topic_0203
application sub category: topic 3295
application sub category: topic 3419
citation: J.CSBJ.2021.04.027
citation: pmcid:PMC8113760
citation: pubmed:34025933
description: AddictGene is an integrated knowledge base for differentially expressed genes associated with psychostimulants,
feature list: operation 2422
feature list: operation 3223
feature list: operation 3431
feature list: operation 3672
software help: tutorial.html

AddTag
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0196
application sub category: topic_0749
application sub category: topic 3168
application sub category: topic 3912
citation: JKAB216
citation: pmcid:PMC8496238
citation: pubmed:34544122
description: AddTag is a two-step approach with supporting software package that facilitates CRISPR/Cas-mediated precision genome editing. CRISPR Cas-induced genome editing is a powerful tool for genetic engineering, however, targeting constraints limit which loci are editable with this method. Since the length of a DNA sequence impacts the likelihood it overlaps a unique target site, precision editing of small genomic features with CRISPR Cas remains an obstacle. We introduce a two-step genome editing strategy that virtually eliminates CRISPR Cas targeting constraints and facilitates precision genome editing of elements as short as a single base-pair at virtually any locus in any organism that supports CRISPR Cas-induced genome editing. Our two-step approach first replaces the locus of interest with an "AddTag" sequence, which is subsequently replaced with any engineered sequence, and thus circumvents the need for direct overlap with a unique CRISPR Cas target site.
feature list: operation_0308
feature list: operation 3096
feature list: operation 3216
is accessible for free: true
license: AGPL-3.0

ADeditome
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3320
application sub category: topic 3512
citation: bbaa384
citation: pmcid:PMC8424397
citation: pubmed:33401309
description: ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer's disease.
feature list: operation_0264
feature list: operation_0433
feature list: operation_0463
feature list: operation 2441
feature list: operation 3223

ADEIP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3295
application sub category: topic 3948
citation: BBAB274
citation: pmcid:PMC8344678
citation: pubmed:34254996
description: An integrated platform of age-dependent expression and immune profiles across human tissues.
feature list: operation_0314
feature list: operation 2436
feature list: operation 3463
feature list: operation 3800
operating system: Linux
operating system: Mac
operating system: Windows

AdelaiDet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic 3382
application sub category: topic 3473
citation: TPAMI.2020.3032166
citation: pubmed:33074804
description: AdelaiDet is an open source toolbox for multiple instance-level recognition tasks on top of Detectron2. All instance-level recognition works from our group are open-sourced here.
feature list: operation 3359
feature list: operation 3436

Adenita
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0611
application sub category: topic_0654
application sub category: topic 3303
citation: GKAA593
citation: pmcid:PMC7470936
citation: pubmed:32692355
description: Adenita is a 3D visualization and modeling toolkit for the in silico design of static and dynamic DNA nanostructures. Based on a multiscale data model, it visualizes DNA-based structures on different abstraction levels and enable users to load and create DNA origami structures and combine them with proteins.
feature list: operation_0570
feature list: operation 2442
feature list: operation 3216
license: BSD-3-Clause

Adenosiland
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 2258
citation: j.ejmech.2012.10.022
citation: pubmed:23127988
description: Adenosiland represents the first attempt of an integrated bioinformatics and chemoinformatics web-resource dedicated to adenosine receptors. This informatics platform provides a wide-ranging of structure based and ligand based query functions to facilitate the exploration of adenosine receptor structures from primary sequences to three-dimensional architectures. Here, we present an overview of Adenosiland platform describing the most valuable searching tools and their functionalities.
feature list: operation 2406
operating system: Linux
operating system: Mac
operating system: Windows
provider: ELIXIR-ITA-PADOVA
software help: help.php
primary contact: Stefano Moro

Animation of Adverse Event Profiles (AdEPro)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web application
application sub category: topic 2269
application sub category: topic 3379
author: Nicole Mentenich
citation: S43441-020-00178-4
citation: pubmed:32529631
description: AdEPro (Animation of Adverse Event Profiles) is an app that (audio-)visualizes adverse events occurring in clinical trials. As this data is usually considered sensitive, this tool is provided as a stand-alone application that can be launched from any local machine on which the data is stored.
feature list: operation_0337
feature list: operation 2422
license: GPL-3.0
software help: adepro.pdf

Adverse drug event presentation and tracking (ADEPT)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0218
application sub category: topic_0769
application sub category: topic 3378
application sub category: topic 3379
citation: OOAA031
citation: pmcid:PMC7660953
citation: pubmed:33215076
description: ADEPT is a tool for a high-sensitivity natural language processing (NLP) pipeline for detecting potential adverse drug events (ADEs) with easily interpretable output for high-efficiency human review and adjudication of true ADEs.
feature list: operation 3778
license: Apache-2.0

Adepth
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0092
application sub category: topic_0154
application sub category: topic_0166
application sub category: topic 2275
application sub category: topic 3382
citation: gkt299
citation: pmcid:PMC3692060
citation: pubmed:23609539
description: Adepth web server provides both depth and height representation of an atom in a macromolecule; it is capable of computing isosurfaces for atomic depths and presenting graphical view of marcomolecular shape at some distance away from the surface.
feature list: operation_0387
feature list: operation_0478
feature list: operation 2950
operating system: Linux
operating system: Mac
operating system: Windows
software help: Adepth tutorial1.pdf
primary contact: Adepth coordinator

ADEPTS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic 3520
citation: s0219720010005099
citation: pubmed:21121022
description: Software package for peptide identification using two different types of MS/MS spectra.
feature list: operation 3631
operating system: Linux
operating system: Mac
operating system: Windows

ADEx: Autoimmune Diseases Explorer
type: SoftwareApplication
input: GEO accession number
  type: FormalParameter
  additional type: data 1147
output: Heat map
  type: FormalParameter
  additional type: data 1636
output: Expression data
  type: FormalParameter
  additional type: data 2603
output: Pathway or network report
  type: FormalParameter
  additional type: data 2984
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3170
application sub category: topic 3295
application sub category: topic 3308
citation: s12859-021-04268-4
citation: pmcid:PMC8223391
citation: pubmed:34167460
description: ADEx: Autoimmune Diseases Explorer is a comprehensive and centralized database for exploring omics data in Autoimmune Diseases. The database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most common autoimmune diseases.
feature list: operation_0313
feature list: operation_0571
feature list: operation 2495
feature list: operation 3431
feature list: operation 3436
feature list: operation 3501
feature list: operation 3927
feature list: operation 3928
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

ADFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0654
application sub category: topic 3168
application sub category: topic 3320
citation: BTAA226
citation: pubmed:32246828
description: ADFinder is an efficient detector of programmed DNA eliminations using NGS high-throughput sequencing data. ADFinder can predict programmed DNA eliminations with relatively low sequencing coverage, detect multiple alternative splicing forms in the same genomic location, and calculate the frequency for each splicing event. This software would facilitate research of programmed DNA eliminations and all down-stream analyses.
feature list: operation_0232
feature list: operation_0264
feature list: operation_0433
feature list: operation 3196

ADGO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0157
application sub category: topic_0203
application sub category: topic 3277
application sub category: topic 3518
citation: btl378
citation: gkr392
citation: pmcid:PMC3125784
citation: pubmed:16837524
citation: pubmed:21624890
description: ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.
feature list: operation 2436
feature list: operation 2495
feature list: operation 3223
feature list: operation 3762
operating system: Linux
operating system: Mac
operating system: Windows
software help: ADGO2
primary contact: ADGO Support

ADH-PPI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Workflow
application sub category: topic_0091
application sub category: topic_0108
application sub category: topic_0128
application sub category: topic 3474
application sub category: topic 3957
citation: j.isci.2022.105169
citation: pmcid:PMC9576568
citation: pubmed:36267921
description: An attention-based deep hybrid model for protein-protein interaction prediction.
feature list: operation_0267
feature list: operation 2492
feature list: operation 3891
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: Tutorial

AdhereR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0092
application sub category: topic_0637
application sub category: topic 3303
application sub category: topic 3375
citation: journal.pone.0174426
citation: shti190479
citation: pmcid:PMC5405929
citation: pubmed:28445530
citation: pubmed:31438176
description: Computation of adherence to medications from Electronic Healthcare Data.
feature list: operation_0224
feature list: operation_0337
operating system: Linux
operating system: Mac
operating system: Windows
software help: AdhereR.pdf
software help: AdhereR-overview.html
software help: ReadMe.md
primary contact: Dan Dediu

AdipoQ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
additional type: Script
application sub category: topic_0153
application sub category: topic 2229
application sub category: topic 3382
application sub category: topic 3407
citation: mbc.E21-11-0592
citation: pmcid:PMC9635306
citation: pubmed:35947507
description: A simple toolbox of two ImageJ plugins for quantifying adipocyte morphology and function in tissues and in vitro.
feature list: operation 3443
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

Adjacency-Matrix-Visualizer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
description: A scalable tool to visualize the adjacency matrix with values on the edges, direction, and the sum of value as the node size.
feature list: operation_0337
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0
primary contact: Chaohan Yang

Adjusted-ADJUST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3418
application sub category: topic 3474
citation: PSYP.13566
citation: pmcid:PMC7402217
citation: pubmed:32185818
description: Adjusted-ADJUST is a script for the automatic identification of artifacts in electroencephalograph (EEG) data.
feature list: operation 3432
feature list: operation 3435
license: GPL-3.0

Adjusted Local Connectivity
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3304
application sub category: topic 3444
description: ALC is a dynamic fMRI connectivity toolbox for single-subject validation.
feature list: operation 3755
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.3
primary contact: Mangor Pedersen

ZMIX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic 3517
citation: VBAE128
citation: pmcid:PMC11632184
citation: pubmed:39664860
description: ZMIX is a software tool for estimating ancestry proportions in genome-wide association studies (GWAS) using only association Z-scores. It offers a novel method to overcome the challenge of inaccessible study reference allele frequencies.
feature list: operation 3226
feature list: operation 3435
feature list: operation 3557
feature list: operation 3659
feature list: operation 3891

adjustPKL
type: SoftwareApplication
input: Peptide mass fingerprint
  type: FormalParameter
  additional type: data_0944
  encoding format: format 3653
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3653
output: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3653
output: Peptide mass fingerprint
  type: FormalParameter
  additional type: data_0944
  encoding format: format 3653
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0092
application sub category: topic 3520
application sub category: topic 3572
description: A tool for adjusting mass spectrometry peaks in PKL file. User can decide whether to shift all spectra or just a single one of the file.
feature list: operation 3203
feature list: operation 3628
operating system: Linux
operating system: Mac
operating system: Windows
software help: adjustpkl

ADL Workbench
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0089
description: ADL Workbench is a compiler and IDE for working with the archetypes and templates written in the Achetype Definition Language (ADL), and based on any reference model, including openEHR, ISO 13606 and CIMI.
is accessible for free: true
license: Apache-2.0
operating system: Windows
software help: adl workbench guide.html
software version: 2.0.6

Anaerobic Digestion Model No. 1 Fast (ADM1F)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0621
application sub category: topic 3068
citation: BIT.28906
citation: pmcid:PMC11895414
citation: pubmed:39717912
description: ADM1F is an open-source platform for fast and stable simulations of anaerobic digestion processes, leveraging PETSc for efficient numerical solutions. It features an iPython interface for model configuration, simulation, data analysis, and visualization, offering a significant speed advantage over conventional methods.
feature list: operation_0244
feature list: operation_0337
feature list: operation 2426

ADME
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3336
application sub category: topic 3373
application sub category: topic 3375
application sub category: topic 3379
citation: https://doi.org/10.1177/24725552211017520
citation: pubmed:34176369
description: Validating ADME QSAR Models Using Marketed Drugs.
feature list: operation_0409
feature list: operation 2428
feature list: operation 3799
operating system: Linux
operating system: Mac
operating system: Windows

ADmeth
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0219
application sub category: topic_0634
application sub category: topic_0654
application sub category: topic 3295
citation: TCBB.2022.3178087
citation: pubmed:35617175
description: A manually curated database for the differential methylation in Alzheimer's disease.
feature list: operation 2421
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

ADMETlab
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2258
application sub category: topic 2275
application sub category: topic 3314
citation: s13321-018-0283-x
citation: pmcid:PMC6020094
citation: pubmed:29943074
description: Provides a user-friendly, freely available web interface for systematic ADMET evaluation of chemical compounds based on a comprehensive database consisting of 288,967 entries.
feature list: operation_0322
operating system: Linux
operating system: Mac
operating system: Windows
software help: interpretation
primary contact: Dong-Sheng Cao

ADMETopt2
type: SoftwareApplication
input: SMILES string
  type: FormalParameter
  additional type: data 2301
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2258
application sub category: topic 3303
application sub category: topic 3336
application sub category: topic 3375
application sub category: topic 3474
citation: s13321-023-00707-x
citation: pmcid:PMC10029263
citation: pubmed:36941726
description: Chemical Rules for Optimization of Chemical Mutagenicity via Matched Molecular Pairs Analysis and Machine Learning Methods.
feature list: operation 2428
feature list: operation 4009
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

admix-kit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic 3056
citation: btae148
citation: pmcid:PMC10980565
citation: pubmed:38490256
description: An integrated toolkit and pipeline for genetic analyses of admixed populations.
feature list: operation 3196
feature list: operation 3891
feature list: operation 3920
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

Admixem
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic 3056
citation: btv700
citation: pubmed:26615212
description: The Admixture simulator is a new forward-time simulator that allows for rapid and realistic simulations of admixed populations with selection.
feature list: operation 2476
operating system: Linux
operating system: Mac
software help: admixem

ADMIXMAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3056
citation: https://doi.org/10.1086/420855
citation: pmcid:PMC1181989
citation: pubmed:15088268
description: Program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred.
feature list: operation 2426
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.html

ADMIXPIPE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Workflow
application sub category: topic_0102
application sub category: topic_0610
application sub category: topic 2885
application sub category: topic 3796
citation: S12859-020-03701-4
citation: pmcid:PMC7391514
citation: pubmed:32727359
description: A method for parsing and filtering VCF files for admixture analysis. The method is able to filters SNPs to allow the delineation of population structure in ADMIXTURE and parses the output for summarization and graphical representation via CLUMPAK.
feature list: operation_0488
feature list: operation 1812
feature list: operation 3196
feature list: operation 3695
license: GPL-3.0
operating system: Linux
operating system: Mac

admixr
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic 2885
citation: btz030
citation: pubmed:30668635
description: Provides a convenient interface for performing reproducible population genetic analyses as implemented by command-line programs in the ADMIXTOOLS software suite.
feature list: operation 1812
feature list: operation 3196
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: admixr
software version: 0.7.1
primary contact: Martin Petr

AdmixSim 2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3056
application sub category: topic 3305
application sub category: topic 3796
citation: S12859-021-04415-X
citation: pmcid:PMC8522168
citation: pubmed:34663213
description: AdmixSim 2 is a forward-time simulator for modeling complex population admixture.
feature list: operation_0487
feature list: operation 2426
feature list: operation 3196
feature list: operation 3891
license: GPL-3.0
software help: AdmixSim2 manual.pdf
primary contact: https://orcid.org/0000-0002-1975-1002

AdmixTools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3056
citation: genetics.112.145037
citation: pmcid:PMC3522152
citation: pubmed:22960212
description: Implements five methods to analyze admixture: the three-population test, D-statistics, F4-ratio estimation, admixture graph fitting, and rolloff. In addition, it computes lower and upper bounds on admixture proportions based on f3-statistics. Contains 6 programs: convertf, qp3Pop, qpBound, qpDstat, qpF4Ratio, and rolloff.
feature list: operation 3197
license: Unlicense
operating system: Linux
operating system: Mac
software help: AdmixTools

Admixture
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3056
citation: gr.094052.109
citation: pmcid:PMC2752134
citation: pubmed:19648217
description: Maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates using a fast numerical optimization algorithm.
feature list: operation 3197
license: Not licensed
operating system: Linux
operating system: Mac
software help: admixture-manual.pdf

admixturegraph
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0092
application sub category: topic 2269
application sub category: topic 3293
citation: btx048
citation: pmcid:PMC5447235
citation: pubmed:28158333
description: Implements tools for building and visualising admixture graphs and for extracting equations from them. These equations can be compared to f- statistics obtained from data to test the consistency of a graph against data – for example by comparing the sign of f_4-statistics with the signs predicted by the graph – and graph parameters (edge lengths and admixture proportions) can be fitted to observed statistics.
feature list: operation_0324
feature list: operation_0567
operating system: Linux
operating system: Mac
operating system: Windows
software help: admixturegraph.pdf
primary contact: Thomas Mailund

ADMO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Ontology
application sub category: topic_0089
application sub category: topic_0602
application sub category: topic_0634
citation: BAAB004
citation: pmcid:PMC7937031
citation: pubmed:33590873
description: Alzheimer Disease Map Ontology (ADMO) is an ontology created from a disease map. ADMO is a formal representation of AD pathophysiology at the molecular scale. It was designed to store and link omics biomedical data.

ADNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3382
application sub category: topic 3473
application sub category: topic 3474
citation: J.NEUNET.2019.12.024
citation: pubmed:31991307
description: An attention-guided denoising convolutional neural network (ADNet), mainly including a sparse block (SB), a feature enhancement block (FEB), an attention block (AB) and a reconstruction block (RB) for image denoising.

ADNI OASIS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3379
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3474
citation: BIOMEDICINES12040896
citation: pmcid:PMC11047992
citation: pubmed:38672253
description: ADNI OASIS is a resource providing MRI data, demographics, and other related information for Alzheimer's disease research. It integrates imaging features and patient demographics for dementia classification.
feature list: operation 2422
feature list: operation 2428

adnuts
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0610
application sub category: topic 2269
application sub category: topic 3474
citation: journal.pone.0197954
citation: pmcid:PMC5967695
citation: pubmed:29795657
description: Bayesian inference using the no-U-turn (NUTS) algorithm.
feature list: operation 2426
operating system: Linux
operating system: Mac
operating system: Windows
software help: adnuts.pdf
primary contact: Cole Monnahan

ADOPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0080
citation: biecoll-jib-2012-200
citation: pubmed:22829571
description: Tool for detecting positively selected amino acid sites from a set of unaligned nucleotide sequence data.
feature list: operation 3092
operating system: Windows
software help: ADOPS
primary contact: Jorge Vieira

ADOPT
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
output: Protein globularity
  type: FormalParameter
  additional type: data 1526
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web application
application sub category: topic_0154
application sub category: topic_0593
application sub category: topic 3306
application sub category: topic 3474
application sub category: topic 3538
citation: lqad041
citation: pmcid:PMC10150328
citation: pubmed:37138579
description: Intrinsic protein disorder prediction through deep bidirectional transformers.
feature list: operation_0272
feature list: operation_0321
feature list: operation_0470
feature list: operation 3904
feature list: operation 4009
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

ADOPT BBMRI-ERIC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic_0769
application sub category: topic 2640
application sub category: topic 3337
application sub category: topic 3577
citation: S-0039-1695793
citation: pmcid:PMC6739205
citation: pubmed:31509880
description: Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC. The Samply.MDR-based ETL tools from ADOPT BBMRI-ERIC.
feature list: operation_0335
feature list: operation 1812
feature list: operation 3283
license: GPL-3.0

ADOpy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2269
application sub category: topic 3361
application sub category: topic 3678
citation: s13428-020-01386-4
citation: pmcid:PMC9335234
citation: pubmed:32901345
description: ADOpy is a Python implementation of Adaptive Design Optimization, which computes optimal designs dynamically in an experiment. Its modular structure permit easy integration into existing experimentation code.
feature list: operation 2426
feature list: operation 3435
feature list: operation 3799
license: GPL-3.0

ADP-Fuse
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0091
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3474
citation: j.compbiomed.2023.107386
citation: pubmed:37619323
description: A novel two-layer machine learning predictor to identify antidiabetic peptides and diabetes types using multiview information.
feature list: operation 2990
feature list: operation 3631
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

ADPedKD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3325
application sub category: topic 3384
application sub category: topic 3418
application sub category: topic 3422
citation: J.EKIR.2019.05.015
citation: pmcid:PMC6732756
citation: pubmed:31517146
description: A Global Online Platform on the Management of Children With ADPKD. Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common monogenic causes of kidney failure with an estimated worldwide prevalence of 1 in 500-2500 live births and affecting approximately 13 million individuals worldwide, representing a major socio-economic medical problem in the world. ADPKD is characterized by the progressive development and enlargement of multiple renal cysts in all nephron segments, progressively leading to end-stage kidney disease (ESKD) in 50% of patients by the age of 60 years. ADPKD arises as a consequence of mutations in the PKD1 (80% of patients) or PKD2 (15% of patients) genes, which encode respectively the proteins polycystin-1 (PC1) and -2 (PC2). Together, working on ADPedKD, we will aim at completing these gaps and having a better understanding of the ADPKD pediatric perspective.
feature list: operation 3196
feature list: operation 3659

adpenetrance
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 2269
application sub category: topic 3305
application sub category: topic 3676
citation: https://doi.org/10.1101/2021.03.16.21253691
description: ADPenetrance is a calculator for variant penetrance using family history of disease and population data. Penetrance is the probability of developing a particular trait given that a person harbours a certain genetic variant or set of variants. This tool uses population-scale data to allow estimation of the penetrance of risk variants associated with autosomal dominant traits.
feature list: operation 3196
feature list: operation 3225
feature list: operation 3435
primary contact: https://orcid.org/0000-0002-4924-7712
primary contact: https://orcid.org/0000-0002-5280-5017

AdpFunChisq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic 3518
application sub category: topic 3895
citation: btac206
citation: pubmed:35561208
description: Adapted Functional Chi-squared test (AdpFunChisq) is a model-free functional dependency measure that uses function direction and strength as evidence for causal inference.
is accessible for free: true
license: LGPL-3.0
operating system: Mac
operating system: Windows

ADPriboDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0078
application sub category: topic_0154
application sub category: topic_0601
application sub category: topic_0602
application sub category: topic_0736
application sub category: topic 2229
application sub category: topic 3071
citation: GKAA941
citation: gkw706
citation: https://doi.org/10.1101/2020.09.24.298851
citation: pmcid:PMC5210603
citation: pmcid:PMC7523110
citation: pmcid:PMC7778992
citation: pubmed:27507885
citation: pubmed:32995784
citation: pubmed:33137182
description: ADPriboDB is a database to facilitate studies in uncovering insights into the mechanisms and biological significance of ADP-ribosylation. ADPriboDB 2.0 serves as a one-stop repository comprising 48 346 entries and 9097 ADP-ribosylated proteins, of which 6708 were newly identified since the original database release.
feature list: operation_0417
feature list: operation 2421
feature list: operation 3431
feature list: operation 3755
software version: 2.0

Adrenaline
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0602
application sub category: topic 2640
application sub category: topic 3305
application sub category: topic 3377
application sub category: topic 3421
citation: S41467-024-47002-3
citation: pmcid:PMC10997660
citation: pubmed:38580683
description: Adrenaline is a resource providing insights into the association between concomitant medication and survival in patients with breast cancer. It utilizes a nationwide French cohort study to identify medications associated with survival outcomes, providing hypotheses for drug influence on breast cancer evolution.
feature list: operation 3503

adsn
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 2229
citation: https://doi.org/10.1101/628347
description: Single Cell Brain Atlas in Human Alzheimer’s Disease.
feature list: operation_0337
feature list: operation_0441
feature list: operation 2436
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Enrico Petretto
primary contact: Jose M. Polo
primary contact: Owen J. L. Rackham

adSplit
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 3053
application sub category: topic 3518
citation: btm322
citation: pubmed:17586546
description: This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.
feature list: operation_0313
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: adSplit.html
software version: 1.44.0
primary contact: Claudio Lottaz

ADTEx
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2640
application sub category: topic 3168
application sub category: topic 3676
citation: https://doi.org/10.1186/1471-2164-15-732
citation: pmcid:PMC4162913
citation: pubmed:25167919
description: Aberration Detection in Tumour Exome (ADTEx) is a tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.
feature list: operation 2238
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial.html
primary contact: Kaushalya Amarasinghe

ADTnorm
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0166
application sub category: topic_0203
application sub category: topic 3512
citation: V1
description: ADTnorm is a normalization and integration method designed for CITE-seq datasets, addressing batch effects in ADT expression. It improves cell-type identification and enables atlas-level analyses by accurately aligning populations and providing utilities for threshold-gating and antibody panel selection.
feature list: operation_0480
feature list: operation 3435

ADToolbox
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3174
application sub category: topic 3375
application sub category: topic 3407
citation: https://doi.org/10.1101/2024.07.16.603753
description: ADToolbox is a Python package for modeling anaerobic digestion metabolism, incorporating metagenomic information to enhance VFA production accuracy. It provides command-line interfaces, a Python API, and facilitates large-scale metagenomic analyses and modeling simulations.
feature list: operation 2426

Advance Resistance Calculator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
description: It can calculate four band and five band resistor's resistance.
feature list: operation 3482
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: Yawar Rehman

Advanced Cell Classifier
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0625
application sub category: topic 2640
application sub category: topic 3298
application sub category: topic 3385
citation: j.cels.2017.05.012
citation: pubmed:28647475
contributor: http://orcid.org/0000-0002-0371-7782
description: Software suite that applies machine-learning and image-analysis methods to high-content data generated by large-scale, cell-based experiments. It features methods to mine microscopic image data, discover new phenotypes, and improve recognition performance.
feature list: operation 3443
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: ACC Documentation 20170620.pdf

Advanced PDB search
type: SoftwareApplication
output: Structure
  type: FormalParameter
  additional type: data_0883
output: Protein structure report
  type: FormalParameter
  additional type: data 1537
output: Database search results
  type: FormalParameter
  additional type: data 2080
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2814
citation: gkv1352
citation: pmcid:PMC4702932
citation: pubmed:26673705
description: Search the PDB.
feature list: operation_0339
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
software help: terms-of-use
software help: http://www.ebi.ac.uk/pdbe-srv/view/search
software version: 1
primary contact: Gerard Kleywegt

ADViSELipidomics
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0153
application sub category: topic_0769
application sub category: topic 3172
application sub category: topic 3407
application sub category: topic 3520
citation: BTAC706
citation: pubmed:36308459
description: ADViSELipidomics is a novel Shiny app for the preprocessing, analysis, and visualization of lipidomics data.
feature list: operation 1812
feature list: operation 3435
feature list: operation 3799
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: ADViSELipidomics book

ADVIT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3382
application sub category: topic 3473
citation: J.FORSCIINT.2020.110345
citation: pubmed:32505803
description: ADVIT is an Automated Dorsum Vein Identification Tool, which helps to perform human identification through hand dorsum vein images. The program can be requested using the form.
feature list: operation 3894
is accessible for free: true

ADVP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3295
application sub category: topic 3305
application sub category: topic 3517
citation: https://doi.org/10.1101/2020.09.29.20203950
description: ADVP is a platform for the public community to browse, search and understand Alzheimer's Disease genetics findings easily. .
feature list: operation 3196
feature list: operation 3226
feature list: operation 3675
feature list: operation 3791

ADZE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2885
application sub category: topic 3056
citation: btn478
citation: pmcid:PMC2732282
citation: pubmed:18779233
description: Program that implements the rarefaction method for analyzing allelic diversity across populations while correcting for sample size differences. Using individual multilocus genotype data on genetic polymorphisms, this tool computes estimates of allelic richness, private allelic richness and private allelic richness for combinations of populations.
feature list: operation_0484
feature list: operation 3227
operating system: Linux
operating system: Mac
software help: adze.html
primary contact: Noah A Rosenberg

AEenrich
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 2269
application sub category: topic 3305
application sub category: topic 3378
application sub category: topic 3400
citation: V1
description: A R package for performing adverse event (AE) enrichment analysis by gene enrichment tests.
feature list: operation 2238
feature list: operation 3501
license: GPL-2.0
software help: AEenrich.pdf

AEGeAn
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0622
citation: https://doi.org/10.1186/1471-2105-13-187
citation: pmcid:PMC3439248
citation: pubmed:22852583
description: The AEGeAn Toolkit provides a bundle of software tools for evaluating gene structure annotations and genome organization.
feature list: operation_0361
feature list: operation 2451
license: ISC
software help: index.html
software version: 0.16.0

AEMDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0634
application sub category: topic_0659
application sub category: topic 3474
citation: BTAA670
citation: pubmed:32726399
description: Implementation of AEMDA for inferring potential disease-miRNA associations.
feature list: operation_0463
feature list: operation 2422
feature list: operation 3792

The Atomic Energy Network (aenet)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0176
application sub category: topic_0593
application sub category: topic 3315
application sub category: topic 3372
application sub category: topic 3474
citation: https://doi.org/10.1063/5.0063880
citation: pubmed:34418919
description: The Atomic Energy NETwork (ænet) package is a collection of tools for the construction and application of atomic interaction potentials based on artificial neural networks (ANN).
feature list: operation 2476
feature list: operation 3891
feature list: operation 4009
is accessible for free: true
license: MPL-2.0
operating system: Linux
software help: tutorial

AeQTL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic_0622
application sub category: topic 3170
application sub category: topic 3676
citation: pmcid:PMC8050802
citation: pubmed:33691015
description: eQTL analysis using region-based aggregation of rare genomic variants.
feature list: operation_0335
feature list: operation 3226
feature list: operation 3227
feature list: operation 3232
feature list: operation 3436
license: MIT

Aequatus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0622
application sub category: topic_0797
citation: https://doi.org/10.1101/055632
description: Aequatus is a homology browser to visualise homologous, orthologous and paralogous gene structures from Ensembl Compara and Ensembl Core databases
feature list: operation_0564
feature list: operation_0567
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: aequatus-user-guide

AESOP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic 2814
citation: j.bpj.2017.04.005
citation: pmcid:PMC5425408
citation: pubmed:28494947
description: Facilitates quantitative comparisons of electrostatics in protein families and describes electrostatic contributions of individual amino acids.
feature list: operation 2487
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.html
primary contact: Dimitrios Morikis

Aevol
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0621
application sub category: topic_0625
application sub category: topic 3299
application sub category: topic 3796
citation: EVAE250
citation: pmcid:PMC11666309
citation: pubmed:39566106
description: Aevol is a computational platform for studying the evolution of digital organisms under different conditions, allowing researchers to understand evolutionary forces and mechanisms shaping genome and transcriptome structures. It was used to test hypotheses relating to mutation rate and population size and their effect on genome reduction.
feature list: operation_0554
feature list: operation 3196
feature list: operation 3745

AFA-Recur
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2269
application sub category: topic 3474
application sub category: topic 3577
citation: euac145
citation: pmcid:PMC10103564
citation: pubmed:36006664
description: AFA-Recur, a machine-learning-based probability score predicting 1-year risk of recurrent atrial arrhythmia after AF ablation
feature list: operation 3359
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

AFAL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0166
application sub category: topic_0602
application sub category: topic 3534
citation: S10822-014-9783-6
citation: pmcid:PMC4241235
citation: pubmed:25085083
description: Web service for profiling amino acids surrounding ligands in proteins.
feature list: operation 2575
operating system: Linux
operating system: Mac
operating system: Windows
software help: faq.html
primary contact: Contact form

AFDB-Cluster
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3697
citation: https://doi.org/10.1101/2024.08.14.607935
description: AFDB-Cluster provides a representation of protein structural clusters derived from the AlphaFold Protein Structure Database (AFDB) and other datasets, facilitating analysis of protein structure-function relationships. The resource offers a way to explore the shared functional landscape across diverse protein data sources.
feature list: operation_0291
feature list: operation_0474
feature list: operation 2844

AfexCore
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Bioinformatics portal
application sub category: topic 3316
contributor: Nirmal Weerapperuma
description: AfexCore brings 12 essential bioinformatics tools into one intuitive GUI - built for researchers who need quick, reliable sequence analysis without the complexity (or price tag) of enterprise software.
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: Beta 2.1.4

AFExNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 2640
application sub category: topic 3170
application sub category: topic 3360
application sub category: topic 3474
citation: TCBB.2021.3066086
citation: pubmed:33720833
description: AFExNet is an adversarial autoencoder for differentiating breast cancer sub-types and extracting biologically relevant genes.
feature list: operation 3432
feature list: operation 3937
license: CC-BY-4.0
primary contact: NeuroSyd

southern Benin Forest Species
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0780
application sub category: topic 3050
application sub category: topic 3810
citation: ARPHAPREPRINTS.E129192
description: This dataset documents the main forest species encountered in southern and central Benin, West Africa, based on field collections and monitoring efforts. It is intended for forestry research and characterization of species abundance in relation to environmental changes.
feature list: operation 3946

affxparser
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3071
application sub category: topic 3518
citation: nmeth.3252
description: Package that parses Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.
feature list: operation_0335
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affxparser.html
software version: 1.46.0
primary contact: Kasper Daniel Hansen

affy
type: SoftwareApplication
input: Gene expression profile
  type: FormalParameter
  additional type: data_0928
  encoding format: format 2058
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 3547
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0092
application sub category: topic_0203
application sub category: topic 3473
citation: microarrays3010001
citation: pmcid:PMC5003452
citation: pubmed:27605027
contributor: http://orcid.org/0000-0001-5282-3250
description: The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions.
feature list: operation 2495
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affy.html
software version: 1.52.0
primary contact: Rafael A. Irizarry

Affy6CNV
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3053
application sub category: topic 3518
description: Affy6CNV is a pipeline for calling CNVs from Affymetrix 6.0 genotyping array data.
feature list: operation 3196
operating system: Linux
operating system: Mac
software help: Manual
software version: 0.0.1

affycomp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 3518
citation: btg410
citation: pubmed:14960458
description: The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.
feature list: operation_0315
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affycomp.html
software version: 1.50.0
primary contact: Rafael A. Irizarry

AffyCompatible
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3489
application sub category: topic 3518
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.
feature list: operation 2409
license: Artistic-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: AffyCompatible.html
software version: 1.34.0
primary contact: Martin Morgan

affyContam
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3365
application sub category: topic 3518
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: Structured corruption of cel file data to demonstrate QA effectiveness.
feature list: operation 2409
license: Artistic-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affyContam.html
software version: 1.32.0
primary contact: V. Carey

affycoretools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 2269
application sub category: topic 3518
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.
feature list: operation 2409
license: Artistic-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affycoretools.html
software version: 1.46.2
primary contact: James W. MacDonald

AffyExpress
type: SoftwareApplication
input: Gene expression profile
  type: FormalParameter
  additional type: data_0928
  encoding format: format 2058
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 3473
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.
feature list: operation 2495
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: AffyExpress.html
software version: 1.40.0
primary contact: Xuejun Arthur Li

AffyGCQC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 3572
citation: s0219720008003400
citation: pubmed:18464325
description: This tool performs an Affymetrix GeneChip Quality Control by implementing a graphical representation of QC metrics recommended by Affymetrix for GeneChip oligonucleotide array technology. Most importantly, it performs extreme studentized deviate statistical tests for the set of arrays being compared in a given experiment, thus providing an objective measure for outlier detection.
feature list: operation 2238
feature list: operation 2495
feature list: operation 3218
operating system: Linux
operating system: Mac
operating system: Windows
software help: prestations

affyILM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 3518
application sub category: topic 3572
citation: https://doi.org/10.1186/1748-7188-4-15
citation: pmcid:PMC2785812
citation: pubmed:19917117
description: Preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.
feature list: operation 2495
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affyILM.html
software version: 1.26.0
primary contact: Fabrice Berger

affyio
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 3071
application sub category: topic 3518
citation: nmeth.3252
description: Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.
feature list: operation_0335
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affyio.html
software version: 1.44.0
primary contact: Benjamin Milo Bolstad

affylmGUI
type: SoftwareApplication
input: Gene expression profile
  type: FormalParameter
  additional type: data_0928
  encoding format: format 2058
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 3547
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0092
application sub category: topic_0203
application sub category: topic 3473
citation: btl025
citation: pubmed:16455752
description: A Graphical User Interface for analysis of Affymetrix microarray gene expression data using the affy and limma packages.
feature list: operation 2495
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affylmGUI.html
software version: 1.48.0
primary contact: http://orcid.org/0000-0001-9221-2892
primary contact: Keith Satterley
primary contact: Yifang Hu

Affymetrix_Error_Rate
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2885
description: Affymetrix_Error_Rate is a simple program that identifies the error rate in files of Affymetrix microarray SNP data
feature list: operation 2495
operating system: Windows
software version: 20111004

Affymetrix NetAffx Analysis Center
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0160
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0632
application sub category: topic 3518
citation: gkg121
citation: pmcid:PMC165568
citation: pubmed:12519953
description: Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.
feature list: operation_0309
feature list: operation_0361
feature list: operation 2422
feature list: operation 3672
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.affx
primary contact: Support

affyPara
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0080
application sub category: topic 3518
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data.
feature list: operation 2478
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affyPara.html
software version: 1.34.0
primary contact: Markus Schmidberger

affyParaEBI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
description: Aan R based pipeline for parallel pre-processing of Affymetrix TM chips. The pipeline starts from a directory containing raw CEL files files and produces Bioconductor R objects containing gene expression measurements suitable for further analysis.
feature list: operation 2409
feature list: operation 2495
operating system: Linux
operating system: Mac
software help: rcloud
software version: 1.0.0
primary contact: Support

affypdnn
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 3053
citation: bti078
citation: pubmed:15509605
description: The package contains functions to perform the PDNN method described by Li Zhang et al.
feature list: operation 3438
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affypdnn.html
software version: 1.48.0
primary contact: Laurent Gautier

AffyPipe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3796
citation: btu486
citation: pmcid:PMC4609010
citation: pubmed:25028724
description: This tool edits SNP probe classes directly while exporting genotypes in PLINK format.
feature list: operation_0484
feature list: operation 3196
operating system: Linux
operating system: Mac
software help: AffyPipe
primary contact: Ezequiel Nicolazzie

affyPLM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0080
application sub category: topic_0203
application sub category: topic 3518
citation: omi.2006.10.358
citation: pubmed:17069513
description: A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.
feature list: operation 2426
feature list: operation 2428
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affyPLM.html
software version: 1.50.0
primary contact: Ben Bolstad

AffyProbeMiner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0632
application sub category: topic 3179
citation: btm360
description: AffyProbeMiner is to re-define chip definition files (CDFs) for Affymetrix chips taking into account the most recent genomic sequence information. It re-groups probes in Affymetrix chips into probe sets according to a list of non-redundant verified complete coding sequences available in GenBank and RefSeq. Pre-computed CDFs for several chips are available for download.
feature list: operation 2495
operating system: Linux
software help: 2385.full.pdf
software version: 1.0

affyQCReport
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3518
application sub category: topic 3572
citation: nmeth.3252
citation: pmcid:PMC4509590
citation: pubmed:25633503
description: This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.
feature list: operation 2428
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: affyQCReport.html
software version: 1.52.0
primary contact: Craig Parman

AffyRNADegradation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0099
application sub category: topic 3518
application sub category: topic 3572
citation: bts629
citation: pmcid:PMC3530908
citation: pubmed:23097420
description: The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.
feature list: operation 2428
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: AffyRNADegradation.html
software version: 1.20.0
primary contact: Mario Fasold

AFid
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Plug-in
application sub category: topic 3168
application sub category: topic 3382
application sub category: topic 3934
citation: BTAA780
citation: pubmed:32931552
description: A tool for automated identification and exclusion of autofluorescent objects from microscopy images.
feature list: operation 2422
feature list: operation 3443
software help: AFid User Guide for ImageJ.pdf
software help: AFid in Matlab.pdf

AFLAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Workflow
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic_0625
application sub category: topic 3673
citation: https://doi.org/10.1101/2020.09.14.296525
description: The Assembly Free Linkage Analysis Pipeline (AFLAP) was designed to build genetic maps using k-mers. This pipeline takes raw reads as an input, compares the composition (Jellyfish hashes) of the two parents and identifies uniquely segregating k-mers. AFLAP may be applied to any organism for which a mapping population is available.
feature list: operation_0282
feature list: operation_0523
feature list: operation_0525
feature list: operation 3196
feature list: operation 3216
license: MIT

AFLPinSilico
type: SoftwareApplication
input: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
  encoding format: format 1929
output: Nucleic acid sequence
  type: FormalParameter
  additional type: data 2977
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2885
citation: btg090
citation: pubmed:12691992
description: Simulating AFLP fingerprints.
feature list: operation 3202
operating system: Linux
operating system: Mac
operating system: Windows
provider: ugent.be
software help: aflpinsilico
software version: 2
primary contact: http://orcid.org/0000-0002-3985-4981

AFM Image Analysis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3070
application sub category: topic 3314
application sub category: topic 3318
application sub category: topic 3344
application sub category: topic 3382
description: Atomic Force Microscopy Image Analysis
feature list: operation 3443
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0.0.0
primary contact: Prashant Patil

AFnetwork
type: SoftwareApplication
input: Sequence distance matrix
  type: FormalParameter
  additional type: data_0870
output: Pathway or network
  type: FormalParameter
  additional type: data 2600
  encoding format: format 3556
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3293
citation: f1000research.10225.2
citation: pmcid:PMC5224691
citation: pubmed:28105314
description: Alignment-free network of 143 Bacteria and Archaea genomes.
feature list: operation_0567
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: READ ME.txt
primary contact: http://orcid.org/0000-0002-3729-8176

AFP-LSE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0154
application sub category: topic_0621
application sub category: topic_0623
application sub category: topic 3474
application sub category: topic 3512
citation: S41598-020-63259-2
citation: pmcid:PMC7188683
citation: pubmed:32345989
description: Antifreeze Proteins Prediction Using Latent Space Encoding of Composition of k-Spaced Amino Acid Pairs.
feature list: operation_0418
feature list: operation 3891
feature list: operation 3937

AFProPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: https://doi.org/10.1101/2024.04.28.591577
description: Prediction of antifreeze proteins (AFPs)

AFQ-Browser
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0092
application sub category: topic 2229
application sub category: topic 3334
citation: s41467-018-03297-7
citation: pmcid:PMC5838108
citation: pubmed:29507333
description: Browser-based visualization tools for AFQ results.
feature list: operation 3744
operating system: Linux
operating system: Mac
operating system: Windows
software help: AFQ-Browser
primary contact: Yeatman Lab

AFRbase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0078
application sub category: topic_0199
application sub category: topic_0621
citation: btad677
citation: pmcid:PMC10656092
citation: pubmed:37947313
description: Database of protein mutations responsible for antifungal resistance.
feature list: operation_0224
feature list: operation_0306
feature list: operation_0337
feature list: operation 3227
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

African Human Microbiome Portal
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0089
application sub category: topic 3174
application sub category: topic 3277
application sub category: topic 3697
application sub category: topic 4012
citation: BAAD092
citation: pmcid:PMC10782148
citation: pubmed:38204360
description: The African Human Microbiome Portal (AHMP) is a public web portal providing curated metagenomic metadata related to African human microbiome samples. It offers search and retrieval operations and supports metadata search and access.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3431

AFSE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic_0820
application sub category: topic 2275
application sub category: topic 3047
citation: BBAC077
citation: pubmed:35348582
description: An integrated web-based platform for molecular modeling and screening
feature list: operation_0269
feature list: operation 3937
feature list: operation 3938
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

AFST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0654
application sub category: topic 3512
citation: https://doi.org/10.1186/1472-6750-12-16
description: AFST(Abnormality Filtering and Sequence Trimming for ESTs)is a software tool using a pattern analysis approach.
feature list: operation 3192
feature list: operation 3695
operating system: Linux
operating system: Windows
software version: 1.0

afterqc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3572
citation: s12859-017-1469-3
citation: pmcid:PMC5374548
citation: pubmed:28361673
description: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair.
feature list: operation 3218
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

AFTM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0736
application sub category: topic_0820
application sub category: topic 2815
citation: baad008
citation: pmcid:PMC10013729
citation: pubmed:36917599
description: The AFTM database reports the transmebrane segments identified by AlphaFold structural models of human proteins and compares them to those in the UniProt database and the Human Transmembrane Proteome (HTP) database.
feature list: operation_0269
feature list: operation_0417
feature list: operation_0420
feature list: operation_0477
feature list: operation 2241
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Qian Cong

Assembling the Fungal Tree of Life (AFTOL)
type: SoftwareApplication
input: Species name
  type: FormalParameter
  additional type: data 1045
input: Genus name
  type: FormalParameter
  additional type: data 1870
output: Organism report
  type: FormalParameter
  additional type: data 2530
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0621
citation: ajb.91.10.1446
citation: pubmed:21652303
description: Fungal structural and biochemical database.
feature list: operation_0224
operating system: Linux
operating system: Mac
operating system: Windows
software help: resources.php
primary contact: Dr. Joseph Spatafora

Agalma
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0194
application sub category: topic_0622
application sub category: topic 3308
citation: https://doi.org/10.1186/1471-2105-14-330
citation: pmcid:PMC3840672
citation: pubmed:24252138
description: Automated tool that constructs matrices for phylogenomic analyses. It builds alignments of homologous genes and preliminary species trees from genomic and transcriptome data.
feature list: operation_0310
feature list: operation 3258
operating system: Linux
software help: agalma
software version: 0.6.0

AgAnimalGenomes
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic 2885
application sub category: topic 3170
application sub category: topic 3500
application sub category: topic 3512
citation: S00335-023-10008-1
citation: pmcid:PMC10382368
citation: pubmed:37460664
description: AgAnimalGenomes.org provides tools based on JBrowse and Apollo that allow livestock genomics researchers to browse and manually annotate livestock genome assemblies. While a login is required to edit and create new annotations with Apollo, anyone can view the genomes and all data tracks (e.g. genes, gene expression, functional annotation, QTL, SNP, repeats).
feature list: operation_0525
feature list: operation 3096
feature list: operation 3208
feature list: operation 3216
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows

AgBase
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0203
application sub category: topic_0621
application sub category: topic_0780
application sub category: topic 3500
citation: gkq1115
citation: pmcid:PMC3013706
citation: pubmed:21075795
description: AgBase provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.
feature list: operation_0314
feature list: operation 2436
feature list: operation 3672
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.pl
primary contact: AgBase Support

AGDEX
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic_0622
citation: btr362
citation: pmcid:PMC3137228
citation: pubmed:21697127
description: A tool to evaluate agreement of differential expression for cross-species genomics.
feature list: operation_0315
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: AGDEX.html
software version: 1.22.0
primary contact: Cuilan lani Gao

AGE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3175
citation: btq713
citation: pmcid:PMC3042181
citation: pubmed:21233167
description: Tool that implements an algorithm for optimal alignment of sequences with SVs.
feature list: operation_0292
license: CC-BY-NC-4.0
operating system: Linux
operating system: Mac
software help: age
primary contact: Abyzov Alexej

AgeAnno
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic 2229
application sub category: topic 3295
application sub category: topic 3360
citation: gkac847
citation: pmcid:PMC9825500
citation: pubmed:36200838
description: AgeAnno is a comprehensive and curated database, aiming to provide comprehensive characterizations for aging-related genes across diverse tissue-cell types in human by using single-cell RNA and ATAC sequencing data (scRNA and scATAC). The current version of AgeAnno houses 1 678 610 cells from 28 healthy tissue samples with ages ranging from 0 to 110 years.
feature list: operation 3223
feature list: operation 3501
feature list: operation 3672
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

AgeGuess
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3068
application sub category: topic 3360
application sub category: topic 3399
application sub category: topic 3474
application sub category: topic 3489
citation: S41597-019-0245-9
citation: pmcid:PMC6823431
citation: pubmed:31672994
description: AgeGuess is a simple online game in which you can post your photos, have other people guess your age, as well as guess the age of other users.
feature list: operation_0337
feature list: operation 3435
license: CC-BY-NC-SA-4.0

AGenDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0621
application sub category: topic_0622
application sub category: topic_0797
application sub category: topic 3168
citation: gkh386
citation: pmcid:PMC441524
citation: pubmed:15215399
description: AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.
feature list: operation_0232
feature list: operation_0292
feature list: operation_0448
feature list: operation 2454
operating system: Linux
operating system: Mac
operating system: Windows
software help: agenda
primary contact: Alexander Sczyrba

AGENT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 3512
application sub category: topic 3957
citation: https://doi.org/10.1101/2021.04.28.441830
description: AGENT is the the Arabidopsis Gene Regulatory Network Tool for Exploring and Analyzing GRNs.
feature list: operation_0239
feature list: operation 2437
feature list: operation 3925

AgeStructure
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3056
application sub category: topic 3399
citation: j.1558-5646.2010.00953.x
citation: pubmed:20100220
description: Computer program for estimating the generation interval, effective size, variances and covariances of lifetime number of offspring of an age structured population with overlapping generations.
feature list: operation_0487
feature list: operation_0488
feature list: operation 3196
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: agestructure
primary contact: Dr Jinliang Wang

AggloIndel
type: SoftwareApplication
input: Genome map
  type: FormalParameter
  additional type: data 1288
  encoding format: format 2572
output: Nucleic acid features
  type: FormalParameter
  additional type: data 1276
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0160
author: Maureen Smith
author: Roland Wittler
citation: 1471-2164-14-s1-s12
citation: pmcid:PMC3549816
citation: pubmed:23369161
description: This tool to detect structural variations is specifically designed to cluster short-read paired-end data into possibly overlapping predictions for deletions and insertions. It does not make any assumptions on the composition of the data, such as the number of samples, heterogeneity or polyploidy. Taking paired ends mapped to a reference genome as input, it merges mappings to clusters based on a similarity score that takes both the putative location and size of an indel into account.
feature list: operation_0291
feature list: operation 3202
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
provider: BiBiServ
provider: Bielefeld University
provider: CeBiTec
software help: agglodel
software version: 1

aggregate_scores_in_intervals
type: SoftwareApplication
input: Annotation track
  type: FormalParameter
  additional type: data 3002
  encoding format: format 3005
input: Data
  type: FormalParameter
  additional type: data_0006
  encoding format: format 3475
output: Data
  type: FormalParameter
  additional type: data_0006
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0622
application sub category: topic 3572
citation: gkw343
citation: f1000research.1114334.1
citation: pmcid:PMC4987906
citation: pubmed:27137889
description: Such as phastCons, GERP, binCons, and others for a set of genomic intervals.
feature list: operation 2428
feature list: operation 3436
operating system: Linux
operating system: Mac
operating system: Windows
software help: https://galaxy.pasteur.fr/root
software version: 1.1.3
primary contact: Galaxy Support Team

aggregateBioVar
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3518
author: 0000-0001-7079-334X
author: https://orcid.org/0000-0002-7777-4165
citation: btab337
citation: pmcid:PMC8504643
citation: pubmed:33970215
contributor: https://orcid.org/0000-0001-7544-5109
description: aggregateBioVar is a R library for differential gene expression analysis for multi-subject single cell RNA sequencing studies.
feature list: operation_0315
feature list: operation 3196
feature list: operation 3223
feature list: operation 3436
license: GPL-3.0

Aggregation of particles in 2D grid using global control
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3315
application sub category: topic 3444
description: This code solves the aggregation problem using global inputs given N particles in a 2D environment.
feature list: operation 3436
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 2.0.0.0
primary contact: Aaron T. Becker's Robot Swarm Lab

AggreProt
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic 3510
citation: gkae420
description: AggreProt is a web server to predict and engineer protein aggregation. The tool provides a per-residue numerical aggregation propensity value and an overall protein aggregation propensity profile. Along with the protein solvent accessibility area and its transmembrane propensity, AggreProt predictions aid the users on designing soluble proteins.
is accessible for free: true
license: Proprietary
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.0

AGHmatrix
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3517
application sub category: topic 3974
citation: btad445
citation: pmcid:PMC10371492
citation: pubmed:37471595
description: AGHmatrix software is an R-package to build relationship matrices using pedigree (A matrix) and/or molecular markers (G matrix) with the possibility to build a combined matrix of Pedigree corrected by Molecular (H matrix). The package works with diploid and autopolyploid data.
feature list: operation 3196
feature list: operation 3891
is accessible for free: true
license: GPL-3.0

AGILE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0622
application sub category: topic 3168
citation: btq648
citation: pubmed:21088030
description: A hash table based high throughput sequence mapping algorithm for longer 454 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process.
feature list: operation_0492
feature list: operation_0496
feature list: operation 3198
is accessible for free: true
operating system: Linux
software help: usage
primary contact: Misra S.

AgileExomeFilter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3056
application sub category: topic 3676
citation: humu.22490
citation: pmcid:PMC4285299
citation: pubmed:24307375
description: Enables the rapid filtering, screening and sorting of variants derived from an exome sequencing experiment, to allow the rapid detection of possible deleterious variants.
feature list: operation 3197
operating system: Windows
software help: guide.php

AgileFileConverter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3168
description: AgileFileConverter converts varaint data in tab delimited text files, typically supplied by commercial NGS service providers, into the format used by AgileGeneFilter, AgileVariantViewer and AgileFileViewer
feature list: operation_0335
operating system: Windows
software help: guide.php
software version: 20130213

AgileGeneFilter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0078
application sub category: topic_0654
description: AgileGeneFilter allows sequence variants exported from AgileVariantViewer or AgileAnnotator to be filtered, by first identifying the proteins that are affected by the sequence variants and then performing a textual data search on these proteins, using information downloaded from the UNI-Prot web page.
feature list: operation 2421
operating system: Windows
software help: guide.php
software version: 20120105

AgileGenotyper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic_0654
application sub category: topic 2885
description: AgileGenotyper will create a pseudo-microarray SNP genotyping file from an ordered SAM file containing exon sequence data. The file will contain the genotype data at over 0.5 million SNP sites previously identified by the 1000 Genomes project. Such a file can then be used as a data source for a mapping program designed for analyzing Affymetrix microarray SNP data.
feature list: operation 2429
feature list: operation 3196
operating system: Windows
software help: guide.php
software version: 20130204

AgilePairedEndReadsCombiner
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0080
description: AgilePairedEndReadsCombiner reads a matching pair of fasta or fastq files created from a paired end sequence run which used PCR products as the library template and combines the data to produce a single read file contain data equivalent to the whole PCR product.
feature list: operation_0335
operating system: Windows
software help: AgilePairedEndReadsCombiner
software version: 20140923

AgilePindelFilter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0080
application sub category: topic 3056
application sub category: topic 3676
citation: humu.22490
citation: pmcid:PMC4285299
citation: pubmed:24307375
description: Enables the rapid filtering, screening and sorting of indel variants derived from an exome sequencing experiment to allow the rapid detection of possible deleterious variants.
feature list: operation 3197
operating system: Windows
software help: guide.php

AgileQualityFilter
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3168
description: AgileQualityFilter performs a number of pre-alignment tasks on sequence data from an Illumina GA-II clonal sequencer. The primary function of AgileQualityFilter is to remove low quality sequence data before alignment to a reference sequence.
feature list: operation_0335
feature list: operation 2428
feature list: operation 2928
operating system: Windows
software help: guide.php
software version: 20121127

agilp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
description: This script normalises a set of gene expression data files against a predefined reference data set. The normalisation uses LOESS regression. The major assumption is that the actual data and the reference set have a similar epxression frequency distribution. Typically, the reference set used the is average of a large number of datasets such as the output of Baseline script in this package.
feature list: operation 3435
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: agilp.pdf
software version: 3.12.0
primary contact: Benny Chain

AgiMicroRna
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0080
application sub category: topic_0659
citation: https://doi.org/10.1186/1471-2164-12-64
citation: pmcid:PMC3037903
citation: pubmed:21269452
description: Processing and Analysis of Agilent microRNA data.
feature list: operation 2409
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: AgiMicroRna.html
software version: 2.24.0
primary contact: Pedro Lopez-Romero

AGImpute
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3512
citation: btae068
citation: pmcid:PMC10877090
citation: pubmed:38317025
description: Imputation of scRNA-seq data based on a hybrid GAN with dropouts identification.
feature list: operation_0313
feature list: operation_0314
feature list: operation 3557
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

AgiND
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3518
description: The AgiND (Agilent Normalization and Diagnostic Package) R library was developped for diagnosis and normalization of one channel and two channel Agilent microarrays.
feature list: operation 2428
feature list: operation 2495
feature list: operation 3435
operating system: Linux
operating system: Windows
software help: AgiND user guide.pdf
software version: 1.0.7

Aging Atlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0121
application sub category: topic_0208
application sub category: topic 3170
application sub category: topic 3173
application sub category: topic 3399
citation: gkaa894
citation: pmcid:PMC7779027
citation: pubmed:33119753
description: Aging Atlas is a curated biomedical database comprising a range of aging-related multi-omics datasets (i.e. transcriptomics, single-cell transcriptomics, epigenomics, proteomics, and pharmacogenomics), as well as bioinformatics tools to query and visualize these datasets.
feature list: operation 2421
feature list: operation 2422
feature list: operation 2495

aging mouse brain
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3304
application sub category: topic 3308
application sub category: topic 3399
citation: S41593-019-0491-3
citation: pubmed:31551601
description: Single-cell transcriptomic profiling of the aging mouse brain | Methodios Ximerakis, Scott L. Lipnick, Brendan T. Innes, Sean K. Simmons, Xian Adiconis, Danielle Dionne, Brittany A. Mayweather, Lan Nguyen, Zachary Niziolek, Ceren Ozek, Vincent L. Butty, Ruth Isserlin, Sean M. Buchanan, Stuart S. Levine, Aviv Regev, Gary D. Bader, Joshua Z. Levin, and Lee L. Rubin
feature list: operation 1812
feature list: operation 2436
feature list: operation 3258

AgingBank
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0659
application sub category: topic 3173
application sub category: topic 3308
application sub category: topic 3360
application sub category: topic 3500
citation: bbac438
citation: pubmed:36239391
description: A manually curated knowledgebase and high-throughput analysis platform that provides experimentally supported multi-omics data relevant to aging in multiple species.
feature list: operation 3223
feature list: operation 3463
feature list: operation 3792
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

AgingReG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0219
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3068
application sub category: topic 3300
citation: BAAD064
citation: pmcid:PMC10558184
citation: pubmed:37805704
description: Curated database of aging regulatory relationships in humans.
feature list: operation_0224
feature list: operation 2437
feature list: operation 3672
is accessible for free: true
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows

AGLN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic 3382
citation: tip.2022.3166673
citation: pubmed:35436194
description: A framework called Attention guided Global enhancement and Local refinement Network (AGLN) to improve the encoder-decoder network for image segmentation.
feature list: operation 3436
feature list: operation 3629
is accessible for free: true
license: MIT

AgMata
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0154
application sub category: topic_0634
application sub category: topic 3300
application sub category: topic 3306
citation: BTZ912
citation: pubmed:31904854
description: Accurate prediction of protein beta-aggregation with generalized statistical potentials.
feature list: operation_0272
feature list: operation_0303
feature list: operation 3436

AGNOSTOS-DB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0769
application sub category: topic 3174
application sub category: topic 3293
application sub category: topic 3697
application sub category: topic 3941
citation: https://doi.org/10.1101/2021.06.07.447314
description: Resource to unlock the uncharted regions of the coding sequence space.
feature list: operation_0310
feature list: operation 2421
feature list: operation 2422
feature list: operation 3432
software help: agnostos-tutorial

AGODB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0108
application sub category: topic_0203
application sub category: topic_0219
application sub category: topic_0621
application sub category: topic_0736
citation: BAAC078
citation: pmcid:PMC9448894
citation: pubmed:36068786
description: AGODB is a comprehensive domain annotation database of argonaute (Ago) proteins, which contains extensive information about 1902 Ago proteins manually extracted from research articles and public databases.
feature list: operation_0224
feature list: operation_0303
feature list: operation 2436
feature list: operation 3778
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

AGORA
type: SoftwareApplication
input: Species tree
  type: FormalParameter
  additional type: data 3272
input: Gene tree
  type: FormalParameter
  additional type: data 3271
input: Gene report
  type: FormalParameter
  additional type: data_0916
output: Genome report
  type: FormalParameter
  additional type: data 2711
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0084
application sub category: topic_0194
application sub category: topic 3299
citation: s41559-022-01956-z
citation: pmcid:PMC9998269
citation: pubmed:36646945
description: AGORA stands for “Algorithm for Gene Order Reconstruction in Ancestors” . AGORA is used to generate ancestral genomes for the Genomicus online server for gene order comparison, and has been in constant use in the group since.
feature list: operation 3745
is accessible for free: true
license: CECILL-C
operating system: Linux
operating system: Mac
primary contact: http://orcid.org/0000-0001-7032-5650
primary contact: 0000-0002-8209-173X
primary contact: https://orcid.org/0000-0002-7860-3560

aGOtool
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0121
application sub category: topic 3520
citation: nmeth.3621
citation: pubmed:26513550
description: A Gene Ontology enrichment tool, specifically designed for the abundance bias in Mass Spectrometry (MS) based proteomics data. This site can be used for functional annotation enrichment for proteomics data. It contains tools for abundance corrected functional enrichment and supports the following categories: GO-terms, UniProt-keywords, KEGG-pathways, Reactome, WikiPathways, InterPro, Pfam, PubMed Publications, Diseaeses, Tissues, and Compartments.
feature list: operation 2414
feature list: operation 3501
feature list: operation 3928
operating system: Linux
operating system: Mac
operating system: Windows
software help: agotool.org
software version: 0.2
primary contact: http://orcid.org/0000-0001-5794-0456

agplus
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0204
application sub category: topic_0749
citation: btv322
citation: pubmed:25995229
description: Simple command-line tool that enables rapid and flexible production of text tables tailored for aggregation plots from which users can easily design multiple groups based on user-definitions such as regulatory regions or transcription initiation sites.
feature list: operation_0337
feature list: operation 3436
operating system: Linux
operating system: Mac
software help: agplus

agptools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0622
description: Agptools is a suite of tools for performing edits to an AGP file during this manual curation stage of genome assembly.
feature list: operation_0231
feature list: operation_0525
feature list: operation 2409
feature list: operation 3216
license: MIT
software help: agptools
software version: 0.0.1

agReg-SNPdb
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0204
application sub category: topic_0749
application sub category: topic 2885
application sub category: topic 3500
application sub category: topic 3810
citation: BIOLOGY10080790
citation: pmcid:PMC8389679
citation: pubmed:34440019
description: A Database of Regulatory SNPs for Agricultural Animal Species.
feature list: operation_0420
feature list: operation_0440
feature list: operation_0484
feature list: operation 3661
operating system: Linux
operating system: Mac
operating system: Windows

agReg-SNPdb-Plants
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0749
application sub category: topic_0780
application sub category: topic 2885
application sub category: topic 3517
application sub category: topic 3810
citation: biology11050684
citation: pmcid:PMC9138521
citation: pubmed:35625412
description: A database storing SNPs and their predicted impact on transcription factor (TF) binding in promoter regions for different crops.
feature list: operation_0440
feature list: operation_0484
feature list: operation 3196
feature list: operation 3661
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

agriGO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0089
application sub category: topic_0203
application sub category: topic_0621
application sub category: topic 1775
application sub category: topic 3512
citation: gkq310
citation: pmcid:PMC2896167
citation: pubmed:20435677
description: Integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.
feature list: operation 2436
feature list: operation 2454
feature list: operation 3501
feature list: operation 3672
operating system: Linux
operating system: Mac
operating system: Windows
software help: manual.php
primary contact: Qi You (Administrator)
primary contact: Qi You (Bug report)
primary contact: Tian Tian (Administrator)

AGRIS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0203
application sub category: topic_0204
application sub category: topic_0602
application sub category: topic_0749
application sub category: topic_0780
citation: gkq1120
citation: pmcid:PMC3013708
citation: pubmed:21059685
description: Comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively.
feature list: operation_0438
feature list: operation_0441
feature list: operation 1781
feature list: operation 3439
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Agris team

AgroSeek
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3174
application sub category: topic 3697
application sub category: topic 3810
application sub category: topic 3837
citation: S12859-021-04035-5
citation: pmcid:PMC7944603
citation: pubmed:33691615
description: AgroSeek is a system for computational analysis of environmental metagenomic data and associated metadata.
feature list: operation_0362
feature list: operation 2422
feature list: operation 3482

AgrVATE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0114
application sub category: topic_0154
application sub category: topic_0194
application sub category: topic_0199
application sub category: topic 3293
citation: SPECTRUM.01334-21
citation: pmcid:PMC8768832
citation: pubmed:35044202
description: AgrVATE is a tool for rapid identification of Staphylococcus aureus agr locus type and also reports possible variants in the agr operon.
feature list: operation_0265
feature list: operation_0435
feature list: operation_0579
is accessible for free: true
license: MIT
operating system: Linux
operating system: Windows

AGTAR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic 3170
citation: J.COMPBIOMED.2021.104646
citation: pubmed:34274894
description: AGTAR is a program that uses adapted genetic algorithm to assemble and quantify transcripts based on RNA-seq data.
feature list: operation 3258
feature list: operation 3680
feature list: operation 3800
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

AgTC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic_0780
application sub category: topic 3077
application sub category: topic 3810
application sub category: topic 4045
citation: FPLS.2024.1265073
citation: pmcid:PMC10915008
citation: pubmed:38450403
description: AgTC is an open-source tool that generates comma-separated value file templates for standardized data collection in plant science research. It facilitates data collection and management, offering flexibility for various experimental setups and streamlining the data processing pipeline.
feature list: operation 3196
feature list: operation 3435
feature list: operation 3436

AH-DB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0102
application sub category: topic 2814
application sub category: topic 3678
citation: gkr940
citation: pmcid:PMC3245139
citation: pubmed:22084200
description: Database of protein structure pairs (apo-holo structure pairs) before and after binding. AH-DB is designed to provide an easy and unified way to prepare apo-holo structure pair data for studies. Data is generated by identifying/mapping molecules in Protein Data Bank (PDB) entries.
feature list: operation_0320
feature list: operation 2406
feature list: operation 2429
feature list: operation 3282
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: AH-DB team

AHD2FHIR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic_0089
application sub category: topic_0218
application sub category: topic_0769
application sub category: topic 3384
application sub category: topic 3400
citation: shti220026
citation: pubmed:35672965
description: A REST service for mapping text analysis results from Averbis Health Discovery to FHIR resources.
feature list: operation_0306
license: Apache-2.0
operating system: Linux

AHLF
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0601
application sub category: topic 3474
application sub category: topic 3520
citation: https://doi.org/10.1101/2020.05.19.101345
description: Ad hoc learning of fragmentation patterns in mass spectra detects post-translationally modified peptides prior to database search. Deep learning model (Temporal conv net, using dilated conv layers) detects post-translational modified peptides based on their ms/ms spectrum.
feature list: operation 3644
feature list: operation 3646
feature list: operation 3755
feature list: operation 3860
license: MIT

AHMII
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0621
application sub category: topic 3301
application sub category: topic 3339
application sub category: topic 3340
citation: pubmed:12824404
description: This tool offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.
feature list: operation_0224
feature list: operation 2409
feature list: operation 2421
feature list: operation 3431

AhNGE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: https://doi.org/10.1101/2021.01.30.428929
description: AhNGE is a Database for Arachis hypogaea nodule developmental gene expression.
feature list: operation_0314
feature list: operation 2421
feature list: operation 2422
feature list: operation 3672

AHoJ: Apo Holo Protein Search
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web API
additional type: Web application
application sub category: topic_0736
application sub category: topic 2814
application sub category: topic 3534
citation: btac701
citation: pmcid:PMC9750100
citation: pubmed:36282546
description: Webserver & command-line tool for search and alignment of APO (unbound) protein structures from HOLO (bound) forms and vice versa. Features: customizable search of Apo-Holo pairs in the PDB, alignment to the query structure, batch mode for fast parallel dataset processing, visualization via Molstar and PyMol, public documented REST-API.
feature list: operation 2421
feature list: operation 2422
feature list: operation 4009
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software version: 0.4.7

AHTPDB
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0202
application sub category: topic 3376
citation: gku1141
citation: pmcid:PMC4383949
citation: pubmed:25392419
description: Manually curated database of experimentally validated Antihypertensive peptides (AHTPs) with comprehensive information that includes: sequence, inhibitory concentration (IC50), log value of inhibitory concentration (pIC50) and toxicity.
feature list: operation_0226
feature list: operation 2409
software help: info2.php
software help: main help.php
primary contact: DR. Gajendra P. S. Raghava

AHTpin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0128
citation: gkv1116
citation: pmcid:PMC4702812
citation: pubmed:26538599
description: AHTpin is an in silico method developed to predict and design efficient antihypertensive peptides.
feature list: operation 2415
software help: index.php

AHTPs
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic 3335
application sub category: topic 3474
citation: s12539-022-00521-3
citation: pubmed:35474167
description: Accurate prediction of anti-hypertensive peptides based on convolutional neural network and gated recurrent unit
feature list: operation_0267
feature list: operation_0433
feature list: operation 3927
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

AI-biopsy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
additional type: Web application
application sub category: topic_0634
application sub category: topic 2640
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3474
citation: jmri.27599
citation: pmcid:PMC8360022
citation: pubmed:33719168
description: A Deep Learning Approach to Diagnostic Classification of Prostate Cancer Using Pathology-Radiology Fusion. cloud_download Download test images. To run the AI-biopsy framework please follow these steps:. process and result folders from ML training (Not included in this repository). Pre-trained Models of CNN architectures should be downloaded from the "Pre-trained Models" part of https://github.com/wenwei202/terngrad/tree/master/slim#pre-trained-models and be located in your machine (e.g. GitHub_AI-biopsy/scripts/slim/run/checkpoint). The files for pre-trained models are available under the column named "Checkpoint". For accurate results, we recommend the use of axial images with a visible prostate gland. Also, 7 slices per patient are used in voting system to measure the accuracy of the trained model for individual patients. ||| CORRECT NAME OF TOOL COULD ALSO BE 'h4AI-biopsy'
feature list: operation 3443
license: MIT

AI-CT-COVID-19
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2640
application sub category: topic 3384
application sub category: topic 3452
application sub category: topic 3474
citation: https://doi.org/10.1101/2020.05.10.20096073
description: AI-CT-COVID-19 is a collaborative online AI engine for precise CT-based COVID-19 diagnosis using federated learning to provide people worldwide an effective AI model for precise CT-COVID diagnosis.

AI-Driver
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0199
application sub category: topic_0622
application sub category: topic 2640
application sub category: topic 3577
citation: LQAA084
citation: pmcid:PMC7671397
citation: pubmed:33575629
description: AI-Driver (AI-based driver classifier) is an ensemble method for predicting the driver status of somatic missense mutations based on 23 pathogenicity features. AI-Driver is an ensemble method for identifying driver mutations in personal cancer genomes.
feature list: operation_0331
feature list: operation 3227

AI4AMP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Web application
application sub category: topic_0154
application sub category: topic 3373
application sub category: topic 3474
citation: https://doi.org/10.1101/2020.12.17.423359
description: AI4AMP is a sequence-based antimicrobial peptides (AMP) predictor based on PC6 protein encoding method and deep learning.
feature list: operation 2492
feature list: operation 3927

AIAP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic_0749
application sub category: topic 3393
application sub category: topic 3940
citation: j.gpb.2020.06.025
citation: pmcid:PMC9040017
citation: pubmed:34273560
description: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis.
feature list: operation_0337
feature list: operation 3218
feature list: operation 3222
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

AIBench
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3474
citation: j.cmpb.2009.12.003
citation: pubmed:20047774
description: Lightweight, non-intrusive MVC-based Java application framework that eases the connection, execution and integration of operations with well defined input/output.
feature list: operation 2409
operating system: Linux
operating system: Mac
software help: docs

AIBL Distance-to-Boundary Novelty Detection
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3360
application sub category: topic 3384
application sub category: topic 3474
application sub category: topic 3517
citation: FNAGI.2024.1285905
citation: pmcid:PMC11057441
citation: pubmed:38685909
description: The AIBL Distance-to-Boundary model uses novelty detection and distance metrics to identify individuals at risk of developing Alzheimer's disease based on data from the AIBL study. It includes a GUI for non-technical stakeholders and a distance-to-boundary strategy for risk assessment.
feature list: operation 3196
feature list: operation 3799

AID-HS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0634
application sub category: topic 3421
application sub category: topic 3444
citation: ANA.27089
citation: pmcid:PMC11683179
citation: pubmed:39543853
description: AID-HS is an open-source pipeline for detecting and lateralizing hippocampal sclerosis in temporal lobe epilepsy, producing clinically-relevant reports based on MRI scans.
feature list: operation 2428
feature list: operation 3659
feature list: operation 3890

AIDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic_0154
application sub category: topic_0166
application sub category: topic_0196
application sub category: topic_0736
citation: btv092
citation: gku369
citation: pmcid:PMC4086082
citation: pmcid:PMC4481839
citation: pubmed:24831546
citation: pubmed:25701568
description: AIDA: Ab Initio Domain Assembly Server attempts to find the best domain arrangements while maintaining chain connectivity. The server also supports structure assembly from sequence only and restraint-guided simulation producing a final assembly satisfying user-specified inter-domain distance restraints.
feature list: operation_0246
feature list: operation_0303
feature list: operation_0310
feature list: operation_0476
feature list: operation_0478
operating system: Linux
operating system: Mac
operating system: Windows
software help: explain.html
primary contact: Adam Godzik

AIDD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0102
application sub category: topic_0769
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3334
citation: https://doi.org/10.1101/2020.01.22.915348
citation: s12859-020-03888-6
description: Automated Isoform Diversity Detector (AIDD) is pipeline for investigating transcriptome diversity of RNA-seq data. AIDD incorporates open source tools into a static virtualbox to ensure reproducability in RNA-seq analysis. AIDD explores editome by mapping both ADAR and APOBEC editing sites on a global and local level and produces publication ready visualization of ADAR editing landscapes.
feature list: operation 3096
feature list: operation 3680
feature list: operation 3891

AIDE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic_0749
application sub category: topic 2640
application sub category: topic 3384
application sub category: topic 3444
application sub category: topic 3474
citation: S41467-021-26216-9
citation: pmcid:PMC8501087
citation: pubmed:34625565
description: AIDE (Annotation-effIcient Deep lEarning) is a deep learning framework for automatic medical image segmentation with imperfect datasets, including those having limited annotations, lacking target domain annotations, and containing noisy annotations. Automatic segmentation of medical images plays an essential role in both scientific research and medical care. Deep learning approaches have presented encouraging performances, but existing high-performance methods typically rely on very large training datasets with high-quality manual annotations, which are normally difficult or even impossible to obtain in many clinical applications.
feature list: operation 3435
feature list: operation 3443
feature list: operation 3553
license: LGPL-2.1
primary contact: https://orcid.org/0000-0001-5400-2093
primary contact: https://orcid.org/0000-0002-0575-6523
primary contact: https://orcid.org/0000-0002-8558-5102

AIDeveloper
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3070
application sub category: topic 3382
application sub category: topic 3421
application sub category: topic 3474
application sub category: topic 3934
citation: https://doi.org/10.1101/2020.03.03.975250
description: AIDeveloper is a software tool that allows you to train, evaluate and apply deep neural nets for image classification within a graphical user-interface (GUI).
feature list: operation_0337
feature list: operation 3443
feature list: operation 3802
license: BSD-3-Clause

AIdrug2cov
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0202
application sub category: topic 3336
application sub category: topic 3373
application sub category: topic 3379
application sub category: topic 3400
citation: CHEMRXIV.12531314.V2
description: AIdrug2cov is a network representation learning-based methodology to discover drug mechanism and anti-inflammatory response for patients with COVID-19.

AIDrugApp
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic 2275
application sub category: topic 3375
application sub category: topic 3474
citation: CHEMRXIV.13312661.V1
description: Artificial Intelligence-based Web-App for Virtual Screening of Inhibitors against SARS-COV-2.
feature list: operation_0337
feature list: operation 3938

AIHF-nomogram
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3324
application sub category: topic 3412
application sub category: topic 3577
citation: fimmu.2023.1130362
citation: pmcid:PMC10229817
citation: pubmed:37266419
description: An easy-to-use AIHF-nomogram to predict advanced liver fibrosis in patients with autoimmune hepatitis.
feature list: operation 2428
feature list: operation 3659
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

AiiDA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2258
application sub category: topic 3332
application sub category: topic 3473
application sub category: topic 3524
citation: s41597-020-00638-4
citation: s13321-017-0242-y
citation: pmcid:PMC5686034
citation: pmcid:PMC7479590
citation: pubmed:29138947
citation: pubmed:32901044
description: Sophisticated framework designed from scratch to be a flexible and scalable infrastructure for computational science. Being able to store the full data provenance of each simulation, and based on a tailored database solution built for efficient data mining implementations, AiiDA gives the user the ability to interact seamlessly with any number of HPC machines and codes thanks to its flexible plugin interface, together with a powerful workflow engine for the automation of simulations.
feature list: operation 3762
license: MIT
operating system: Linux
operating system: Mac
software help: latest
primary contact: Andrius Merkys

AILDE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 2275
application sub category: topic 3299
application sub category: topic 3332
application sub category: topic 3336
application sub category: topic 3371
citation: J.ISCI.2020.101179
citation: pmcid:PMC7267738
citation: pubmed:32498019
description: AILDE (Auto In Silico Ligand Directing Evolution) server is developed according to the CSO (Computational Substitution Optimization) protocol, which was designed to automatically perform computational substitution, energy minimization, and binding affinity evaluation. Auto In Silico Ligand Directing Evolution to Facilitate the Rapid and Efficient Discovery of Drug Lead.
feature list: operation_0531
feature list: operation 3216
feature list: operation 3938
software help: help

AIM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3518
citation: tnb.2003.817023
citation: pubmed:15376910
description: The Automatic Image Processing for Microarrays tool is designed for uncalibrated microarray gridding and quantitative image analysis. Uncalibrated microarray image analysis supports integration of expression data from different sources and can improve reproducibility.
feature list: operation_0571
feature list: operation 3443
is accessible for free: true
license: Unlicense
operating system: Linux
software help: aim

AIME
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 2640
application sub category: topic 3474
citation: JOURNAL.PCBI.1009826
citation: pmcid:PMC8820645
citation: pubmed:35081109
description: Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments.
feature list: operation_0463
feature list: operation 3792
feature list: operation 3891
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

AIMEE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic_0632
application sub category: topic_0749
application sub category: topic_0821
application sub category: topic 3336
application sub category: topic 3474
citation: BBAB301
citation: pmcid:PMC8385923
citation: pubmed:34368837
description: A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe.
feature list: operation_0478
feature list: operation 3937
feature list: operation 4009
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows

aiMeRA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3315
application sub category: topic 3512
application sub category: topic 3519
citation: https://doi.org/10.1101/2020.01.30.925800
description: A generic modular response analysis R package and its application to estrogen and retinoic acid receptors crosstalk.
feature list: operation 3799
feature list: operation 3927
software help: aiMeRA Manual.pdf

AIModules
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic_0621
application sub category: topic_0659
application sub category: topic_0749
application sub category: topic 3169
application sub category: topic 3512
citation: V1
description: AIModules enables you to find transcription factor binding sites (TFBSs) and modules on DNA using own matrices or the JASPAR 2022 database.
feature list: operation_0238
feature list: operation_0239
feature list: operation_0337
feature list: operation_0445
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows

AIMS
type: SoftwareApplication
input: Gene expression profile
  type: FormalParameter
  additional type: data_0928
  encoding format: format 2058
output: Disease report
  type: FormalParameter
  additional type: data 1622
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 2269
application sub category: topic 2640
citation: dju357
citation: pubmed:25479802
description: This package contains the necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). The assignments could be done on individual samples as well as on dataset of gene expression data.
feature list: operation_0315
license: Artistic-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: AIMS.html
software version: 1.6.0
primary contact: Eric R Paquet

AIONER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0218
application sub category: topic_0634
application sub category: topic_0780
application sub category: topic 3473
citation: BTAD310
citation: pmcid:PMC10212279
citation: pubmed:37171899
description: All-in-one scheme-based biomedical named entity recognition using deep learning.
feature list: operation_0335
feature list: operation 3280
feature list: operation 3625
feature list: operation 3778
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

aiproteomics
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
application sub category: topic 3474
description: Package containing several tools, datasets and ML models for (phospho-)proteomics.
feature list: operation 2426
license: Apache-2.0
software version: 0.2.0

AIPW
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2269
application sub category: topic 3305
application sub category: topic 3474
citation: kwab207
citation: pmcid:PMC8796813
citation: pubmed:34268567
description: An R Package for Augmented Inverse Probability Weighted Estimation of Average Causal Effects
feature list: operation 3435
feature list: operation 3659
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

Atlas of Inflammation-Resolution (AIR)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3172
application sub category: topic 3400
citation: j.mam.2020.100894
citation: https://doi.org/10.1101/2020.01.27.921882
citation: pmcid:PMC7733955
citation: pubmed:32893032
description: The Atlas of Inflammation-Resolution (AIR) is a web application for capturing an essential part ofacute inflammation and inflammation resolution research.
feature list: operation_0306
feature list: operation_0337
feature list: operation 2421

AIRBP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0108
application sub category: topic_0128
application sub category: topic_0659
application sub category: topic 3474
application sub category: topic 3512
citation: https://doi.org/10.1101/2020.03.10.985416
description: Accurate identification of RNA-binding proteins using machine learning techniques.
feature list: operation_0303
feature list: operation 3767
feature list: operation 3901

Aird
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 3318
application sub category: topic 3360
application sub category: topic 3520
citation: https://doi.org/10.1101/2020.10.14.338921
description: Aird is a new format for mass spectrometry data storage. It is an opensource and computation-oriented format with controllable precision, flexible indexing strategies, and high compression rate for m/z and intensity pairs. Aird provides a novel compressor call ZDPD for m/z data compression,which makes up an amazing compression rate. Compared with Zip, m/z data is about 55% lower in the Aird on average. Aird is a computational friendly algorithm. Through SIMD optimization, the decoding speed of Aird is much higher than that of Zip. AirdPro is opensource under the MulanPSL2 license.
feature list: operation_0335
feature list: operation 3215
feature list: operation 3860

AirLab
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic 2229
application sub category: topic 2830
application sub category: topic 3077
citation: s13059-016-1006-0
description: Cloud-based platform to manage and share antibody-based single-cell research.
feature list: operation 1812
feature list: operation 2421
license: CC-BY-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: http://www.airlaboratory.ch/#/
primary contact: Support

AirLift
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0102
application sub category: topic 2885
application sub category: topic 3168
citation: https://doi.org/10.1101/2021.02.16.431517
description: AirLift is a pipeline that updates mapped reads from one reference genome to another.
feature list: operation_0523
feature list: operation 3198
feature list: operation 3227

airpart
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3452
author: https://orcid.org/0000-0002-5061-7581
citation: https://doi.org/10.1101/2021.10.15.464546
contributor: https://orcid.org/0000-0001-8401-0545
description: Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets.
feature list: operation 3197
feature list: operation 3658
feature list: operation 3659
feature list: operation 3799
is accessible for free: true
license: GPL-2.0
primary contact: https://orcid.org/0000-0002-5061-7581

airpg
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0084
application sub category: topic_0622
application sub category: topic_0780
application sub category: topic 2229
application sub category: topic 3473
citation: S12859-021-04309-Y
citation: pmcid:PMC8379869
citation: pubmed:34418956
description: A Python package for automatically accessing the inverted repeats of thousands of plastid genomes stored on NCBI Nucleotide.
feature list: operation_0237
feature list: operation_0361
feature list: operation 2422
feature list: operation 3431
feature list: operation 3802
is accessible for free: true
license: GPL-3.0
operating system: Linux

airr_tools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Github repository for the paper "T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases" by Høye et al.

AIRRscape
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Web application
application sub category: topic_0160
application sub category: topic 2830
application sub category: topic 3930
application sub category: topic 3966
citation: journal.pcbi.1010052
citation: pmcid:PMC9524643
citation: pubmed:36126074
description: An interactive tool for exploring B-cell receptor repertoires and antibody responses. To run AIRRscape, clone the repo and open the app.R file in your RStudio, then click "Run App". As a Shiny app, it can run as a window of RStudio, or as a tab in a web browser (recommended).
feature list: operation_0252
feature list: operation_0480
feature list: operation 3436
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

AIRRSHIP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 2229
application sub category: topic 2815
application sub category: topic 3127
citation: btad365
citation: pmcid:PMC10272706
citation: pubmed:37279738
description: Simulating human B cell receptor repertoire sequences.
feature list: operation_0451
is accessible for free: true
license: AGPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: airrship.readthedocs.io

Ais
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0077
application sub category: topic_0078
application sub category: topic 2229
application sub category: topic 3452
citation: https://doi.org/10.1101/2024.04.04.586917
description: Ais is a tomogram segmentation package designed for high performance and accessibility. It streamlines segmentation workflows, including particle picking for subtomogram averaging and generating segmentations of cellular architecture, and is available as a GitHub repository with trained models.
feature list: operation_0337
feature list: operation_0479
feature list: operation 3646

AIScaffold
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic 3047
application sub category: topic 3303
citation: ACS.JCIM.0C00867
citation: pubmed:33356237
description: AIScaffold is a web-based tool for scaffold diversification using the deep generative model. AIScaffold can perform large-scale diversification in several minutes and recommend the top 500 molecules. Features such as site-specific diversification are also supported. This tool can facilitate the scaffold diversification process for medicinal chemists, thereby accelerating drug design.
feature list: operation_0337
feature list: operation 3216
feature list: operation 3938

AIscEA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3173
application sub category: topic 3940
citation: btac683
citation: pmcid:PMC9710555
citation: pubmed:36250795
description: AIscEA (Alignment-based Integration of single-cell gene Expression and chromatin Accessibility) a computational method that integrates single-cell gene expression and chromatin accessibility measurements using their biological consistency.
feature list: operation_0314
feature list: operation_0496
feature list: operation 3432
license: CC-BY-4.0

AISO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0089
application sub category: topic 3383
citation: https://doi.org/10.1186/2041-1480-5-50
citation: pmcid:PMC4290088
citation: pubmed:25584184
description: Interactive image segmentation tool designed to allow curators of biological specimens to segment and annotate image data with ontology terms.
feature list: operation 3443
feature list: operation 3553
operating system: Linux
operating system: Mac
operating system: Windows
software help: planteome.org

AITAC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3168
citation: FGENE.2020.00458
citation: pmcid:PMC7205152
citation: pubmed:32425990
description: AITAC is a method for accurately infer tumor purity and absolute copy numbers in a tumor sample by using high-throughput sequencing (HTS) data.
feature list: operation 3196
feature list: operation 3233
feature list: operation 3435
license: GPL-3.0

AITANA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Plug-in
application sub category: topic 3474
description: AITANA is a platform to facilitate the investigation, development, training and inference of predictive models of Machine Learning and Artificial Intelligence, optimizing the computing resources with the use of a set of tools and methodologies. AITANA wants to minimize the times of training and find the solution of a Machine Learning project with the use of a complete platform to provide an abstraction for computational resources and infrastructure.
license: Proprietary
software version: v6.0

AITL
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0208
application sub category: topic 2640
application sub category: topic 3379
application sub category: topic 3474
citation: btaa442
citation: https://doi.org/10.1101/2020.01.24.918953
citation: pmcid:PMC7355265
citation: pubmed:32657371
description: Adversarial Inductive Transfer Learning (AITL) is a deep neural network method for addressing discrepancies in input and output space between the pre-clinical and clinical datasets.
feature list: operation_0303
feature list: operation 3435
feature list: operation 3937

AIUPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0601
application sub category: topic_0736
application sub category: topic_0749
application sub category: topic 3306
application sub category: topic 3538
citation: GKAE385
citation: pmcid:PMC11223784
citation: pubmed:38747347
description: AIUPred is a web server and downloadable package that predicts intrinsically disordered protein regions using a combination of energy estimation and deep learning techniques. It builds upon the original IUPred server and scores among the top three single-sequence-based methods.
feature list: operation_0337
feature list: operation_0470
feature list: operation 2575
feature list: operation 3904

AiZynthFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Desktop application
application sub category: topic 3047
application sub category: topic 3314
application sub category: topic 3474
citation: CHEMRXIV.12465371.V1
description: Aizynthfinder is a tool for retrosynthetic planning. The algorithm is based on a Monte Carlo tree search that recursively breaks down a molecule to purchasable precursors. The tree search is guided by a policy that suggests possible precursors by utilizing a neural network trained on a library of known reaction templates.
license: MIT
software help: index.html

AKDESeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0654
application sub category: topic 3168
citation: 1753-6561-7-s7-s7
citation: pmcid:PMC4043421
citation: pubmed:24564977
description: Software for adaptative-bandwidth kernel density estimation for high-throughput sequencing data.
feature list: operation 2238
feature list: operation 2403
operating system: Linux
operating system: Mac
operating system: Windows
software help: Software.html

AKID
type: SoftwareApplication
input: Protein sequence (raw)
  type: FormalParameter
  additional type: data 2974
output: Protein features
  type: FormalParameter
  additional type: data 1277
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web service
application sub category: topic_0080
application sub category: topic_0601
application sub category: topic 3510
citation: bty545
citation: pmcid:PMC6361239
citation: pubmed:30016513
description: AKID is a Deep Neural Network-based method that identifies kinase-specific phosphorylation events at single-kinase level in any given Eukaryotic proteome without prior functional annotation. It automatically detects kinase domains, their residues responsible for target specificity and finally their target peptides.
feature list: operation_0239
feature list: operation_0276
feature list: operation_0417
operating system: Linux
software version: 1.0
primary contact: Luca Parca

AKLIMATE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic 2640
application sub category: topic 2885
application sub category: topic 3474
citation: https://doi.org/10.1101/2020.07.15.205575
description: AKLIMATE is an R package for a stacked kernel learning algorithm that integrates multi-modal data and prior knowledge feature sets.
feature list: operation_0303
feature list: operation 3659
feature list: operation 3928
license: GPL-3.0

AKSmooth
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic_0204
application sub category: topic_0749
application sub category: topic 3673
citation: s0219720014420050
citation: pubmed:25553811
description: Statistical method that can accurately and efficiently reconstruct the single CpG methylation estimate across the entire methylome using low-coverage bisulfite sequencing (Bi-Seq) data.
feature list: operation_0430
operating system: Linux
operating system: Mac
operating system: Windows
software help: AKSmooth

al3c
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3316
application sub category: topic 3500
application sub category: topic 3855
citation: btv393
description: Software for parameter inference using Approximate Bayesian Computation.
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Alexander H. Stram

ALADYN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0166
application sub category: topic_0176
application sub category: topic_0736
application sub category: topic 2814
citation: gkq293
citation: pmcid:PMC2896196
citation: pubmed:20444876
description: Web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. Input is the structure files of two proteins.
feature list: operation_0474
feature list: operation_0477
feature list: operation 2406
feature list: operation 2487
operating system: Linux
operating system: Mac
operating system: Windows
software help: about.php
primary contact: T. Aleksiev

Alamut
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0092
application sub category: topic_0199
application sub category: topic 3325
description: Software that includes powerful bioinformatics applications for genetic analysis and offers a comprehensive solution to the tasks of genomic variants annotation, filtration, interpretation and reporting. It includes Alamut Batch, which is a high-throughput variant annotation engine for NGS data, Alamut Focus, an interactive variant filtration application for NGS analysis and Alamut Visual, a graphical variant interpretation environment used by leading genetic clinicians and researchers around the world.
feature list: operation_0337
feature list: operation 3197
feature list: operation 3661
feature list: operation 3695
is accessible for free: false
license: Proprietary
operating system: Linux
operating system: Mac
operating system: Windows
software help: products

AlbaTraDIS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0203
application sub category: topic_0625
application sub category: topic_0798
application sub category: topic 3697
citation: JOURNAL.PCBI.1007980
citation: pmcid:PMC7390408
citation: pubmed:32678849
description: AlbaTraDIS is a software application for performing rapid large-scale comparative analysis of TraDIS experiments whilst also predicting the impact of inserts on nearby genes. It allows for experiements with multiple conditions to be easily analysed using statistical methods developed in the Bio-TraDIS toolkit.
feature list: operation_0372
feature list: operation_0427
feature list: operation 3196
feature list: operation 3482
license: GPL-3.0

ALBERT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 3053
application sub category: topic 3516
description: C program that estimates genotype relative risks, genotyping error rates and population risk allele frequencies from marker genotype data in case-parent trios. It uses the distribution of trio marker genotypes to compute maximum likelihood estimates for the parameters.
feature list: operation 3196
operating system: Linux
software help: albert doc.pdf

ALCHEMY
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0625
application sub category: topic 2885
application sub category: topic 3053
citation: btq533
citation: pmcid:PMC2982150
citation: pubmed:20926420
description: ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods.
feature list: operation 3196
operating system: Linux
operating system: Mac
software help: alchemy.sourceforge.net
software version: 1.07

AlcoR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
description: Alignment-free simulation, mapping, and visualization of low-complexity regions in FASTA data.

alder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3056
citation: genetics.112.147330
citation: pmcid:PMC3606100
citation: pubmed:23410830
description: alder detects and dates population admixtures based on patterns of linkage disequilibrium.
feature list: operation_0324
license: MIT
operating system: Linux
software help: alder v1.03.tar.gz
software version: 1.03

ALDEx2
type: SoftwareApplication
input: Gene expression profile
  type: FormalParameter
  additional type: data_0928
  encoding format: format 2058
output: Statistical estimate score
  type: FormalParameter
  additional type: data_0951
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0203
application sub category: topic 2269
citation: https://doi.org/10.1186/2049-2618-2-15
citation: pmcid:PMC4030730
citation: pubmed:24910773
description: A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.
feature list: operation 3658
operating system: Linux
operating system: Mac
operating system: Windows
software help: ALDEx2.html
software version: 1.6.0
primary contact: http://orcid.org/0000-0001-5803-3380

Aldy 4
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0208
application sub category: topic_0625
application sub category: topic 3673
application sub category: topic 3958
citation: gr.277075.122
citation: pmcid:PMC9977157
citation: pubmed:36657977
description: An efficient genotyper and star-allele caller for pharmacogenomics.
feature list: operation_0487
feature list: operation 3196
feature list: operation 3227
feature list: operation 3228
feature list: operation 3454
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

ALE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic 3077
citation: s12859-017-1888-1
citation: pmcid:PMC5751806
citation: pubmed:29297276
description: Automated label extraction from GEO metadata.
feature list: operation 2422
feature list: operation 2495
operating system: Linux
operating system: Mac
software help: README.md
primary contact: Jonathan D. Wren

ALEA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3307
citation: btt744
citation: pubmed:24371156
description: A toolbox for allele-specific epigenomics analysis
is accessible for free: true
license: MIT
operating system: Linux
software help: README.md
software version: 1.3
primary contact: Hamid Younesy

aLeaves
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0084
application sub category: topic 3293
application sub category: topic 3500
citation: gkt389
citation: pmcid:PMC3692103
citation: pubmed:23677614
description: Web server supports homolog collection from diverse animal genomes. An input sequence is passed through the server to collect similar sequences for molecular phylogenetic analysis.
feature list: operation_0492
feature list: operation_0499
feature list: operation_0540
feature list: operation_0550
feature list: operation_0554
operating system: Linux
operating system: Mac
operating system: Windows
software help: faq.html
primary contact: Shigehiro Kuraku

AleRax
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0194
application sub category: topic_0623
application sub category: topic 3293
citation: btae162
citation: pmcid:PMC10990685
citation: pubmed:38514421
description: A tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.
feature list: operation_0544
feature list: operation_0553
feature list: operation 3478
feature list: operation 3942
feature list: operation 3947
is accessible for free: true
license: GPL-3.0

ALeS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
citation: BTAA945
citation: pubmed:34107042
description: A software program to generate highly sensitivity seeds
feature list: operation 2430
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

Aletsch
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3512
citation: BTAE215
citation: pmcid:PMC11211816
citation: pubmed:38940157
description: Aletsch is a software resource for assembling RNA-seq data, particularly useful for multiple bulk or single-cell samples. It employs bridging and graph-decomposition algorithms to restore missed junctions and leverage supporting information across samples.
feature list: operation_0310
feature list: operation 3799

ALEXA-Seq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3320
citation: nmeth.1503
citation: pubmed:20835245
description: Alternative Expression Analysis by massively parallel RNA sequencing
feature list: operation 3800
license: GPL-3.0
operating system: Linux
software help: ALEXA-Seq Manual v.1.17.pdf
primary contact: Malachi Griffith
primary contact: Marco A. Marra

AlexandrusPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0622
application sub category: topic_0769
application sub category: topic 3293
application sub category: topic 3316
citation: evad187
citation: pmcid:PMC10612477
citation: pubmed:37831426
description: Pipeline for the automated detection of orthologous gene clusters and subsequent positive selection analysis.
feature list: operation_0324
feature list: operation 3663
is accessible for free: true

alfaNET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0121
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3810
application sub category: topic 3957
citation: IJMS22158342
citation: pmcid:PMC8348475
citation: pubmed:34361108
description: A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria.
feature list: operation 2421
feature list: operation 2489
feature list: operation 2492
feature list: operation 3461
feature list: operation 3925
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html

ALFATClust
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0080
application sub category: topic_0623
application sub category: topic_0749
application sub category: topic 3174
citation: s12859-022-04643-9
citation: pmcid:PMC8969259
citation: pubmed:35354426
description: A biological sequence clustering tool with dynamic threshold
feature list: operation_0289
feature list: operation_0291
feature list: operation_0491
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Windows

Alfie
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0621
application sub category: topic 3050
application sub category: topic 3174
application sub category: topic 3474
application sub category: topic 3500
citation: https://doi.org/10.1101/2020.06.29.177634
description: Alfie is an alignment-free, kingdom level taxonomic classifier for DNA barcode data. Alfie classifies sequences using a neural network which takes k-mer frequencies (default k = 4) as inputs and makes kingdom level classification predictions.
feature list: operation 1812
feature list: operation 3200
feature list: operation 3460
feature list: operation 3472
license: GPL-3.0

Alfred
type: SoftwareApplication
input: Alignment
  type: FormalParameter
  additional type: data 1916
  encoding format: format 2572
output: Text data
  type: FormalParameter
  additional type: data 2526
  encoding format: format 1921
  encoding format: format 3464
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0091
application sub category: topic 3053
author: https://orcid.org/0000-0001-5773-5620
citation: bty1007
citation: pmcid:PMC6612896
citation: pubmed:30520945
description: BAM Statistics, Feature Counting and Annotation
feature list: operation_0258
feature list: operation_0292
feature list: operation_0361
feature list: operation_0564
is accessible for free: true
license: BSD-3-Clause
operating system: Linux
operating system: Mac
software help: alfred

ALFRED-G
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 2269
application sub category: topic 3293
application sub category: topic 3299
citation: s12859-017-1658-0
citation: pmcid:PMC5471951
citation: pubmed:28617225
description: Distance Estimator for Phylogenetic Inference.
feature list: operation_0324
license: Apache-2.0
operating system: Linux
operating system: Mac
software help: phylo
primary contact: Sharma V. Thankachan

Alfresco
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0080
application sub category: topic_0654
citation: gr.10.8.1148
citation: pmcid:PMC310917
citation: pubmed:10958633
description: Alfresco‘s (FRont-End for Sequence COmparison) aim is to develop a new visualisation tool that allows effective comparative genome sequence analysis. The program will compare multiple sequences from putitatively homologous regions in different species. Results from various different existing analysis programs, such as gene prediction, protein homology and regulatory sequence prediction programs shall be visualised and used to find corresponding sequence domains.
feature list: operation_0337
feature list: operation 2403
feature list: operation 2423
feature list: operation 2424
feature list: operation 2451
feature list: operation 2454
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Niclas Jareborg

alfy
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
citation: btr176
citation: pubmed:21471011
description: Computer program for comparing one or more query DNA sequences to a set of subject sequences. For each query sequence the output consists of a list of intervals indicating the closest homologue among the set of subject sequences.
feature list: operation_0224
feature list: operation 2451
operating system: Linux
operating system: Mac
software help: node1.html

ALGAEFUN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic 3169
application sub category: topic 3170
application sub category: topic 3295
application sub category: topic 3810
citation: https://doi.org/10.1101/2021.08.14.456338
description: AlgaeFUN - MicroAlgae Functional Annotation Web based Tool.
feature list: operation 2436
feature list: operation 3223
feature list: operation 3431
feature list: operation 3680
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

AlgaePath
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0602
application sub category: topic_0780
application sub category: topic 3168
application sub category: topic 3308
application sub category: topic 3407
citation: https://doi.org/10.1186/1471-2164-15-196
citation: pmcid:PMC4028061
citation: pubmed:24628857
description: Comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae.
feature list: operation 2421
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial.php
primary contact: Support

ALGGEN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0196
application sub category: topic_0203
application sub category: topic_0749
application sub category: topic_0798
application sub category: topic 3512
citation: https://doi.org/10.1093/bioinformatics/18.2.333
citation: btg326
citation: gkg605
citation: gkj116
citation: s0907444904030768
citation: pmcid:PMC1347478
citation: pmcid:PMC169011
citation: pubmed:11847087
citation: pubmed:12824386
citation: pubmed:14668235
citation: pubmed:15681873
citation: pubmed:16381947
description: Provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.
feature list: operation_0310
feature list: operation_0438
feature list: operation_0445
feature list: operation_0492
feature list: operation_0526
operating system: Linux
operating system: Mac
operating system: Windows
software help: alggen.lsi.upc.es
primary contact: Xavier Messeguer Peypoch

AlgPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0102
application sub category: topic 1775
application sub category: topic 3474
citation: gkl343
citation: pmcid:PMC1538830
citation: pubmed:16844994
description: Predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.
feature list: operation_0252
feature list: operation_0416
feature list: operation 2429
feature list: operation 3429
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: G. P. S. Raghava

algpred2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic 3307
citation: bbaa294
citation: pubmed:33201237
description: AlgPred 2.0 is an updated version of our old server AlgPred developed for predicting allergenic proteins
feature list: operation 1777
software help: algpred2

Alias
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0078
application sub category: topic_0080
application sub category: topic_0196
application sub category: topic 3068
application sub category: topic 3489
citation: bth241
citation: pubmed:15059813
description: A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.
feature list: operation_0310
feature list: operation_0492
feature list: operation 2479

ALiBaSeq
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0102
application sub category: topic_0194
application sub category: topic_0196
application sub category: topic 3293
application sub category: topic 3673
citation: PEERJ.11019
citation: pmcid:PMC8019319
citation: pubmed:33850647
description: Alignment-based sequence extraction software (ALiBaSeq) is designed to retrieve homologous regions from a FASTA file with contigs (e.g., an NGS read assembly file). The retrieval is done based on reading BLAST, HMMER, or LASTZ search tab-delimited output tables or SAM / BAM alignment files and then searching for the results in an assembly file.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3192
feature list: operation 3216
license: MIT
primary contact: Alexander Knyshov

ALICE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
additional type: Web application
application sub category: topic 3304
application sub category: topic 3382
citation: https://doi.org/10.1101/2021.04.06.438576
description: Automatic Labeling of Independent Components in Electroencephalography (ALICE) is a toolbox and crowdsourcing platform.
primary contact: https://orcid.org/0000-0002-0034-0326

AliClu
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic 3168
application sub category: topic 3416
citation: S12911-019-1013-7
citation: pmcid:PMC6938005
citation: pubmed:31888660
description: Temporal sequence alignment for clustering longitudinal clinical data.
feature list: operation_0292
feature list: operation_0552
feature list: operation 3432

ALICO
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0077
application sub category: topic_0080
application sub category: topic 3307
citation: cmb.2010.0220
citation: pubmed:21314455
description: The Alignment Constrained null set generator is a framework to generate randomized versions of an input multiple sequence alignment that preserve some of its crucial features including its dependence structure.
feature list: operation_0292
feature list: operation_0492
feature list: operation 2426
is accessible for free: true
license: Unlicense
operating system: Linux
operating system: Mac
operating system: Windows
software help: alico suppl.html

AlienTrimmer
type: SoftwareApplication
input: DNA sequence (raw)
  type: FormalParameter
  additional type: data 3497
  encoding format: format 1929
input: DNA sequence (raw)
  type: FormalParameter
  additional type: data 3497
  encoding format: format 1930
output: DNA sequence (raw)
  type: FormalParameter
  additional type: data 3497
  encoding format: format 1930
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
author: Alexis Criscuolo
citation: j.ygeno.2013.07.011
citation: f1000research.1114334.1
citation: pubmed:23912058
citation: pubmed:24860597
description: Trimming and clipping FASTQ-formatted read files.
feature list: operation 2478
is accessible for free: true
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: Bioinformatics and Biostatistics Hub
provider: Institut Pasteur
software help: alientrimmer
software version: 0.4.0
primary contact: Alexis Criscuolo

ALIFRITZ
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0084
application sub category: topic_0654
application sub category: topic 3293
citation: https://doi.org/10.1080/10635150590950371
citation: pubmed:16085574
description: ALIFRITZ performs statistical multiple alignment and phylogeny reconstruction simultaneously. It implements a strategy based on simulated annealing which makes use of these models to infer a phylogenetic tree for a set of DNA or protein sequences together with the sequences’ indel history, i.e. their multiple alignment augmented with information about the positioning of insertion and deletion events in the tree.
feature list: operation_0492
operating system: Linux
software version: 1.0

AliGater
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic 3473
application sub category: topic 3517
application sub category: topic 3934
citation: VBAD103
citation: pmcid:PMC10438955
citation: pubmed:37600847
description: Framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data.
feature list: operation 2945
feature list: operation 3937
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: aligater.readthedocs.io

ALIGN
type: SoftwareApplication
input: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1476
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
  encoding format: format 1984
output: Sequence-profile alignment
  type: FormalParameter
  additional type: data_0869
  encoding format: format 1984
output: Sequence alignment (protein)
  type: FormalParameter
  additional type: data 1384
  encoding format: format 1984
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
citation: https://doi.org/10.2174/157016306780136754
citation: pubmed:17311562
description: Pairwise alignment tool.
feature list: operation_0300
feature list: operation_0495
feature list: operation_0496
operating system: Linux
operating system: Mac
operating system: Windows
provider: ELIXIR-ITA-PADOVA
provider: University of Padua, Department of Biomedical Sciences, BioComputing UP lab
software help: help.html
software version: 2.0
primary contact: http://orcid.org/0000-0003-4525-7793

align-cli
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1929
output: Pair sequence alignment
  type: FormalParameter
  additional type: data 1381
  encoding format: format 2330
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
description: align-cli is a tool to assist manual inspection of mass spectra using alignments, isobaric sequences and other information from mass spectrometry.
feature list: operation_0292
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 0.4.0

Align-GVGD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0199
application sub category: topic_0634
application sub category: topic 2885
application sub category: topic 3306
citation: gkj518
citation: jmg.2005.033878
citation: pmcid:PMC1390679
citation: pmcid:PMC2563222
citation: pubmed:16014699
citation: pubmed:16522644
description: A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral. Align-GVGD is an extension of the original Grantham difference to multiple sequence alignments and true simultaneous multiple comparisons.
feature list: operation_0292
feature list: operation_0448
feature list: operation_0492
feature list: operation 3202
feature list: operation 3501
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php
primary contact: Ewy Mathe
primary contact: Sean Tavtigian

Align-m
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0154
application sub category: topic_0199
application sub category: topic 3168
citation: bth116
citation: pubmed:14962914
description: Align-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks.
feature list: operation_0292
feature list: operation_0492
feature list: operation_0496
operating system: Linux
operating system: Windows
software help: align m manual.pdf
primary contact: Ivo Van Walle

Align-paths
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0085
application sub category: topic_0602
citation: S0218213015400035
description: Inference of Pathway Decomposition Across Multiple Species Through Gene Clustering.
feature list: operation 3439
is accessible for free: true
license: MIT
software help: README.md
software version: 1.0
primary contact: https://orcid.org/0000-0002-0222-4273

align3d
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0084
application sub category: topic_0654
application sub category: topic 3382
citation: F1000RESEARCH.16252.3
citation: pmcid:PMC6644830
citation: pubmed:31363407
description: Improved inference of chromosome conformation from images of labeled loci | chromosome conformation reconstructions based on imaged loci | download the align3d files into the Cicada directory | install the GNU Scientific Library
feature list: operation_0487
feature list: operation 3660
feature list: operation 3745
license: GPL-3.0

AlignACE
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0082
application sub category: topic_0654
application sub category: topic 3473
application sub category: topic 3511
application sub category: topic 3512
citation: nbt1098-939
citation: pubmed:9788350
description: Aligns Nucleic Acid Conserved Elements; uses pattern recognition to find elements conserved in a set of DNA sequences; free for non-commercial use with license agreement.
feature list: operation_0239
feature list: operation_0415
feature list: operation 3196
operating system: Linux
operating system: Windows
software help: program notes.txt
primary contact: Maryanne Fenerjian (HMS Office of Technology Licensing contact)
primary contact: Zhou Zhu (questions or comments)

AlignBucket
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic 3510
citation: btv451
citation: pubmed:26231432
description: Software for splitting a protein FASTA file into smaller pieces suitable for alignment with BLAST. The constraint used to optimize the result is the required minimum alignment coverage.
feature list: operation_0292
feature list: operation 3359
operating system: Linux
software help: alignbucket

aligncopy
type: SoftwareApplication
input: Sequence alignment
  type: FormalParameter
  additional type: data_0863
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3071
citation: S0168-9525(00)02024-2
citation: CBO9781139151399
citation: CBO9781139151405
contributor: EMBOSS Contributors
contributor: UK BBSRC
contributor: UK MRC
contributor: Wellcome Trust
description: Read and write alignments.
feature list: operation 2089
funder: UK BBSRC
funder: UK MRC
funder: Wellcome Trust
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
provider: EMBOSS
software help: ch01s01.html
software help: pr02s04.html
software help: aligncopy.html
software version: r6

aligncopypair
type: SoftwareApplication
input: Sequence alignment
  type: FormalParameter
  additional type: data_0863
output: Sequence alignment (pair)
  type: FormalParameter
  additional type: data 1381
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3071
citation: S0168-9525(00)02024-2
citation: CBO9781139151399
citation: CBO9781139151405
contributor: EMBOSS Contributors
contributor: UK BBSRC
contributor: UK MRC
contributor: Wellcome Trust
description: Read and write pairs from alignments.
feature list: operation 2409
funder: UK BBSRC
funder: UK MRC
funder: Wellcome Trust
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
provider: EMBL-EBI
provider: EMBOSS
software help: ch01s01.html
software help: pr02s04.html
software help: aligncopypair.html
software version: r6

AligNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0081
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic 3957
citation: S12859-020-3502-1
citation: pmcid:PMC7672851
citation: pubmed:33203353
description: An R-package for alignment of protein-protein interaction networks.
feature list: operation_0491
feature list: operation_0496
feature list: operation 2492
feature list: operation 3094

AlignGraph
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0160
application sub category: topic_0196
citation: btu291
citation: pmcid:PMC4058956
citation: pubmed:24932000
description: Software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism.
feature list: operation_0310
feature list: operation_0525
feature list: operation 3217
operating system: Linux
software help: AlignGraph

AlignGraph2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0769
citation: BBAB022
citation: pubmed:33621981
description: AlignGraph2 is a tool for genome-assisted reassembly pipeline for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.
feature list: operation_0524
feature list: operation_0525
feature list: operation 3198
feature list: operation 3216
feature list: operation 3798

AlignMe
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0166
application sub category: topic_0736
application sub category: topic_0820
citation: bi101256x
citation: gku291
citation: journal.pone.0057731
citation: pmcid:PMC3587630
citation: pmcid:PMC4086118
citation: pubmed:21073167
citation: pubmed:23469223
citation: pubmed:24753425
description: AlignMe (for Alignment of Membrane Proteins) can be used to examine detailed similarity between homologous proteins even if there is no notable sequence similarity. The predefined gap/weight sets have been optimized for membrane proteins, and so should be particularly useful for these difficult cases.
feature list: operation_0292
feature list: operation_0491
feature list: operation_0492
feature list: operation 2479
operating system: Linux
operating system: Mac
operating system: Windows
software help: AlignMe
primary contact: AlignMe Support

Alignment-Annotator
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0080
application sub category: topic_0092
application sub category: topic_0602
application sub category: topic 3168
citation: gku400
citation: pmcid:PMC4086088
citation: pubmed:24813445
description: Alignment Annotator is a web service which annotates and renders sequence alignments using annotation services and the PDB. The annotated and colorized alignment can be downloaded as an interactive HTML file for web browsers.
feature list: operation_0292
feature list: operation_0337
feature list: operation_0564
operating system: Linux
operating system: Mac
operating system: Windows
software help: aaScriptDemo.php
primary contact: Christoph Gille

AlignmentComparator
type: SoftwareApplication
input: Sequence alignment
  type: FormalParameter
  additional type: data_0863
  encoding format: format 1433
  encoding format: format 1912
  encoding format: format 1929
  encoding format: format 3160
output: Sequence alignment
  type: FormalParameter
  additional type: data_0863
  encoding format: format 3160
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0080
application sub category: topic 3070
application sub category: topic 3307
author: Ben Stöver
contributor: Kai Müller
description: An application to efficiently visualize and annotate differences between alternative multiple sequence alignments of the same dataset.
feature list: operation_0292
feature list: operation_0564
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: License
software version: 1.0.0
primary contact: Ben Stöver

AlignmentViewer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0080
application sub category: topic_0084
application sub category: topic_0160
application sub category: topic_0623
application sub category: topic 3168
citation: F1000RESEARCH.22242.2
citation: pmcid:PMC7570326
citation: pubmed:33123346
description: AlignmentViewer is multiple sequence alignment viewer for protein families with flexible visualization, analysis tools and links to protein family databases. It can handle protein families with tens of thousand of sequences and is particularly suitable for evolutionary coupling analysis, preparing the computation of protein 3D structures and detection of functionally constrained interactions.
feature list: operation_0492
feature list: operation_0564
feature list: operation 2479
license: MIT

alignparse
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0199
application sub category: topic 3168
citation: joss.01915
description: A Python package for parsing complex features from high-throughput long-read sequencing. Align sequences and then parse features. alignparse documentation — alignparse 0.1.2 documentation. alignparse is a Python package written by the Bloom lab. It is designed to align long sequencing reads (such as those from PacBio circular consensus sequencing) to targets, filter these alignments based on user-provided specifications, and parse out user-defined sequence features. For each read that passes the filters, information about the features (e.g. accuracy, sequence, mutations) is retained for further analyses. alignparse is a Python package written by the Bloom lab. It is designed to align long sequencing reads (such as those from PacBio circular consensus sequencing) to targets, filter these alignments based on user-provided specifications, and parse out user-defined sequence features
feature list: operation 1812
feature list: operation 3198
feature list: operation 3695

ALIGNSEC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0078
application sub category: topic_0092
application sub category: topic 2814
citation: btx521
citation: pubmed:28961944
description: Viewing protein secondary structure predictions within large multiple sequence alignments. The module is part of the ANTHEPROT package.
feature list: operation_0570
operating system: Linux
operating system: Mac
operating system: Windows
software help: http://antheprot-pbil.ibcp.fr/anthe_histo.php
primary contact: Gilbert Deleage

AlignStat
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0080
application sub category: topic 2269
citation: s12859-016-1300-6
citation: pmcid:PMC5081975
citation: pubmed:27784265
description: AlignStat is a web-tool and R package for statistical comparison of alternative multiple sequence alignments.
feature list: operation 2451
license: Other
operating system: Linux
operating system: Mac
operating system: Windows
software help: README.md
software version: 1.3.2
primary contact: http://orcid.org/0000-0002-2298-7593

Alignstein
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
citation: giac101
citation: pmcid:PMC9633278
citation: pubmed:36329619
description: LC-MS alignment algorithm based on Wasserstein distance.
is accessible for free: true
license: MIT
software version: 1.0

ALION
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
description: ALION is a sequence alignment tool. Aligns two protein sequences using Needleman-Wunsch global alignment or Smith-Waterman local alignment methods with variable gap penalties and amino acid substitution matrices. Analogous to GCG GAP and BESTFIT programs.
feature list: operation_0292
feature list: operation_0491
feature list: operation_0495
feature list: operation_0496
operating system: Linux
software version: 1.0

alkaligrass
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0196
application sub category: topic_0749
application sub category: topic 3170
application sub category: topic 3293
application sub category: topic 3308
citation: S11427-020-1662-X
citation: pubmed:32180108
description: A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance. A high-quality chromosome-level genome sequence of alkaligrass assembled from Illumina, PacBio and 10× Genomics reads combined with genome-wide chromosome conformation capture (Hi-C) data. The ∼1.50 Gb assembled alkaligrass genome encodes 38,387 protein-coding genes, and 54.9% of the assembly are transposable elements, with long terminal repeats being the most abundant. Comparative genomic analysis coupled with stress-treated transcriptome profiling uncovers a set of unique saline- and alkaline-responsive genes in alkaligrass
feature list: operation_0525
feature list: operation 2429
feature list: operation 2495

Alkemio
type: SoftwareApplication
input: Keyword
  type: FormalParameter
  additional type: data_0968
input: Article ID
  type: FormalParameter
  additional type: data 1088
input: Compound identifier
  type: FormalParameter
  additional type: data 1086
output: Small molecule report
  type: FormalParameter
  additional type: data_0962
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Web service
application sub category: topic 3473
citation: gku432
citation: pmcid:PMC4086102
citation: pubmed:24838570
description: Chemicals prioritization for topics of interest using gene-related PubMed abstracts.
feature list: operation_0305
operating system: Linux
operating system: Mac
operating system: Windows
software help: http://cbdm-01.zdv.uni-mainz.de/~jfontain/cms/
primary contact: Jean Fred Fontaine

ALL-P
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic 3321
citation: pmic.201100660
citation: pubmed:22833229
description: Statistical framework based on a hierarchical modeling that takes into account shared peptide information for estimating protein abundances. It performs a simultaneous analysis of all the quantified peptides, handling the biological and technical errors as well as the peptide effect.
feature list: operation 2406
feature list: operation 2423
feature list: operation 3630
operating system: Linux
operating system: Mac
operating system: Windows
software help: download.php

All2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0622
application sub category: topic 3676
citation: https://doi.org/10.1101/2021.09.29.462281
description: All2 is a tool for filtering variants from all2all comparison of multiple clones or single cells. There are no variant allele frequency and mutation spectrum plots for structural variant mode and the format of the output files will be slightly different from the SNV/INDEL analyses.
feature list: operation_0337
feature list: operation 3227
feature list: operation 3675
is accessible for free: true
license: MIT
primary contact: Alexej Abyzov

AllCCS2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0153
application sub category: topic_0154
application sub category: topic 3047
application sub category: topic 3172
application sub category: topic 3520
citation: ACS.ANALCHEM.3C02267
citation: pubmed:37664900
description: Curation of ion mobility collision cross-section atlas for small molecules using comprehensive molecular representations.
feature list: operation 2421
feature list: operation 3927
feature list: operation 4009
is accessible for free: true

AllCoPol
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Suite
application sub category: topic_0084
application sub category: topic_0102
application sub category: topic 3316
citation: S12859-020-03750-9
citation: pmcid:PMC7542712
citation: pubmed:33028201
description: AllCoPol is a collection of tools for the analysis of polyploids, which allow to infer ancestral allele combinations as well as corresponding subgenome phylogenies.
feature list: operation 3432
feature list: operation 3478
feature list: operation 3840
license: MIT

Allegro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0080
application sub category: topic_0654
application sub category: topic_0749
citation: gkn1064
citation: pmcid:PMC2655690
citation: pubmed:19151090
description: It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.
feature list: operation_0238
operating system: Linux
operating system: Windows
software help: overview.html
software version: 1.0

Allele frequency net
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0199
application sub category: topic_0208
application sub category: topic 2830
application sub category: topic 3056
application sub category: topic 3305
citation: gkq1128
citation: pmcid:PMC3013710
citation: pubmed:21062830
description: The allele frequency net database is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. At present, the system contains data on the frequency of genes from different polymorphic regions such as human leukocyte antigens, killer-cell immunoglobulin-like receptors, major histocompatibility complex Class I chain-related genes and a number of cytokine gene polymorphisms.
feature list: operation_0487
feature list: operation_0542
feature list: operation 3196
feature list: operation 3221
feature list: operation 3227
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Support

AlleleRetain
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3056
application sub category: topic 3299
citation: j.1755-0998.2012.03176.x
citation: pubmed:22925629
description: R package to simulate small populations. Output includes demographic trends and information, probability of retaining a rare allele, and accumulation of inbreeding over the simulated period.
feature list: operation 2426
operating system: Linux
operating system: Mac
operating system: Windows
software help: home

AlleleShift
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3056
citation: PEERJ.11534
citation: pmcid:PMC8212829
citation: pubmed:34178449
description: AlleleShift is an R package to predict and visualize population-level changes in allele frequencies in response to climate change.
feature list: operation_0337
feature list: operation_0554
feature list: operation 3659
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

allelic inclusion
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 2229
application sub category: topic 2269
application sub category: topic 2830
citation: J.CELS.2019.09.006
citation: pubmed:31677971
description: A Bayesian Inference of Allelic Inclusion Rates in the Human T Cell Receptor Repertoire.
feature list: operation 3658

AllelicImbalance
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 3168
application sub category: topic 3170
citation: s12859-015-0620-2
citation: pmcid:PMC4465016
citation: pubmed:26066318
contributor: http://orcid.org/0000-0002-5635-2692
description: Provides a framework for allelic specific expression investigation using RNA-seq data.
feature list: operation 2495
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: AllelicImbalance.html
software version: 1.12.0
primary contact: Jesper R Gadin

Allen Brain Atlas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0203
application sub category: topic 3304
application sub category: topic 3382
application sub category: topic 3444
application sub category: topic 3512
citation: gks1042
citation: pmcid:PMC3531093
citation: pubmed:23193282
description: The Allen Brain Atlas (ABA) project has developed a web-based application designed to aid the intersection of neuroscience and genomics. The ABA Application enables users to access an extensive database of high resolution in situ hybridization (ISH) images from over 10,000 genes, reference atlases in both the sagittal and coronal planes, gene expression masks capturing the intensity of gene expression or signal, and the ability to search for gene expression by anatomic region.
feature list: operation_0224
feature list: operation_0314
feature list: operation_0315
feature list: operation 2495
feature list: operation 3223
operating system: Linux
operating system: Mac
operating system: Windows
software help: index.html
primary contact: Contact Form

Allen Brain Atlas-API
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web API
application sub category: topic_0203
citation: nature05453
citation: pubmed:17151600
description: Integration of gene expression data, connectivity data and neuroanatomical information for the adult and developing brain in mouse, human and non-human primate.
feature list: operation 2495
operating system: Linux
operating system: Mac
operating system: Windows
software help: RESTful+Model+Access+(RMA)
software version: 1

AllEnricher
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0089
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3173
citation: S12859-020-3408-Y
citation: pmcid:PMC7076970
citation: pubmed:32183716
description: A comprehensive gene set function enrichment tool for both model and non-model species. This is a tool designed for functional genomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets, or differential epigenomic modification gene sets etc) are continuously generated. AllEnricher incorporates information from different public resources and provides an easy way for biologists to make sense out of gene lists.
feature list: operation 3223
feature list: operation 3463
feature list: operation 3501
feature list: operation 3928
license: MIT

AllerCatPro
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0130
application sub category: topic_0154
application sub category: topic_0601
application sub category: topic_0804
application sub category: topic 3400
citation: gkac446
citation: pmcid:PMC9252832
citation: pubmed:35640594
description: A web server for predicting protein allergenicity potential.
feature list: operation_0252
feature list: operation_0474
feature list: operation 3092
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
software version: 2.0

ALLERDET
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic_0780
application sub category: topic 3400
application sub category: topic 3474
application sub category: topic 3810
citation: j.jbi.2022.104217
citation: pubmed:36244612
description: A novel web app for prediction of protein allergenicity.
feature list: operation_0252
feature list: operation_0491
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

Allerdictor
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
application sub category: topic 3307
application sub category: topic 3510
citation: btu004
citation: pmcid:PMC3982160
citation: pubmed:24403538
description: Fast and accurate sequence-based allergen prediction tool that models protein sequences as text documents and employs support vector machine in text classification for allergen prediction.
feature list: operation 2479
operating system: Linux
operating system: Mac
operating system: Windows
software help: home
primary contact: Ha Dang

AllergenFP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic 3307
citation: btt619
citation: pubmed:24167156
description: Bioinformatics tool for allergenicity prediction based on a novel descriptor fingerprint approach.
feature list: operation 2423
feature list: operation 2479
operating system: Linux
operating system: Mac
operating system: Windows
software help: method.html
primary contact: Drug Design Group

Allergome
type: SoftwareApplication
input: Identifier
  type: FormalParameter
  additional type: data_0842
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 2331
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0804
citation: s11882-009-0055-9
citation: pubmed:19671381
description: A platform for allergen knowledge.
feature list: operation_0224
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.php

AllerTOP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic 1775
citation: s00894-014-2278-5
citation: pubmed:24878803
description: Server for in silico prediction of allergens based on the main physicochemical properties of proteins.
feature list: operation 2479
operating system: Linux
operating system: Mac
operating system: Windows
software help: method.html
primary contact: Drug Design Group

AllesTM
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0082
application sub category: topic_0154
application sub category: topic_0736
application sub category: topic_0820
application sub category: topic 3474
citation: S12859-020-03581-8
citation: pmcid:PMC7291640
citation: pubmed:32532211
description: AllesTM is an integrated tool to predict almost all structural features of transmembrane proteins that can be extracted from atomic coordinate data. It blends several machine learning algorithms: random forests and gradient boosting machines, convolutional neural networks in their original form as well as those enhanced by dilated convolutions and residual connections, and, finally, long short-term memory architectures.
feature list: operation_0249
feature list: operation_0269
feature list: operation_0303
feature list: operation_0474
feature list: operation 2241
license: MIT

allhic
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3473
application sub category: topic 3474
citation: s41477-019-0487-8
citation: pubmed:31383970
description: Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
feature list: operation 3216
is accessible for free: true
license: BSD-2-Clause
operating system: Linux
operating system: Mac
operating system: Windows

Alliance Genome Resources
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0089
application sub category: topic_0621
application sub category: topic 3068
application sub category: topic 3489
application sub category: topic 3571
citation: GENETICS.119.302523
citation: pmcid:PMC6893393
citation: pubmed:31796553
description: A modern data ecosystem for model organism databases.
feature list: operation 2421
feature list: operation 2422
feature list: operation 3431

Allim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0203
application sub category: topic_0622
application sub category: topic 3053
citation: https://doi.org/10.1111/1755-0998.12110
citation: pmcid:PMC3739924
citation: pubmed:23615333
description: The Allelic imbalance meter tool offers an integrated and user-friendly solution for measuring allele specific gene expression (ASE) within species.
feature list: operation 2495
is accessible for free: true
license: MPL-1.1
operating system: Linux
operating system: Mac
software help: Manual.wiki
software help: allim
primary contact: Christian Schlötterer
primary contact: Ram Vinay Pandey
primary contact: Susanne U. Franssen

AlloFinder
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0602
application sub category: topic 3336
citation: gky374
citation: pmcid:PMC6030990
citation: pubmed:29757429
description: Identifies potential endogenous or exogenous allosteric modulators as well as their characterization in human allosterome. Automatically amalgamates allosteric site identification, allosteric screening and allosteric scoring evaluation of modulator–protein complexes to identify allosteric modulators, followed by allosterome mapping analyses of predicted allosteric sites and modulators in human proteome. Enables identification of allosteric metabolites for metabolic enzymes and screening of potential allosteric compounds for disease-related targets.
feature list: operation_0417
feature list: operation_0482
feature list: operation 3803
software help: help.jsp
software version: 1.01

AlloMAPS 2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0121
application sub category: topic_0199
application sub category: topic_0632
application sub category: topic_0634
application sub category: topic 3577
citation: gkac828
citation: pmcid:PMC9825619
citation: pubmed:36169226
description: The database provides data on the energetics of communication in proteins with well-documented allosteric regulation, allosteric signalling in PDBselect chains, and allosteric effects of mutations.
feature list: operation_0303
feature list: operation_0331
feature list: operation 4009
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows
software help: tutorial

AlloPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic 3534
citation: s12859-015-0771-1
citation: pmcid:PMC4619270
citation: pubmed:26493317
description: Web server uses normal mode analysis and pocket features to predict allosteric pockets on proteins.
feature list: operation 2575
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
provider: hotmail.co.uk
software help: tutorial
software version: 1
primary contact: http://orcid.org/0000-0002-5154-1929

AlloReverse
type: SoftwareApplication
input: Protein structure
  type: FormalParameter
  additional type: data 1460
  encoding format: format 1476
output: Protein property
  type: FormalParameter
  additional type: data_0897
output: Pathway or network report
  type: FormalParameter
  additional type: data 2984
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0209
application sub category: topic 2229
citation: gkad279
citation: pmcid:PMC10320067
citation: pubmed:37070199
description: Web server for multiscale analysis of multiple allosteric regulations.
feature list: operation_0321
feature list: operation 3092
feature list: operation 3928
feature list: operation 4009
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.jsp

Alloscore
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic 2275
citation: pubmed:26803160
description: Web server that predicts the binding affinities of allosteric ligand-protein interactions.
feature list: operation 2406
feature list: operation 2464
feature list: operation 2479
feature list: operation 2575
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.jsp

AlloSigMA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0632
application sub category: topic 2640
citation: GKAA338
citation: pmcid:PMC7319554
citation: pubmed:32392302
description: A web application for exploring and quantifying the effects of allosteric ligand binding and mutations.
feature list: operation_0331
feature list: operation 2575
feature list: operation 3227
software help: tutorial
software version: 2

Allosite
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0082
citation: btt399
citation: pubmed:23842804
description: Tool for the prediction of allosteric sites in proteins.
feature list: operation 2479
feature list: operation 2575
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.jsp

AlloViz
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0128
application sub category: topic_0176
application sub category: topic_0593
application sub category: topic_0820
application sub category: topic 3292
citation: J.CSBJ.2024.04.047
citation: pmcid:PMC11087696
citation: pubmed:38736696
description: AlloViz is a Python package for computing, analyzing, and visualizing protein allosteric communication networks. It integrates existing methods and facilitates the calculation of consensus-like scores based on multiple structural aspects of allosteric networks.
feature list: operation_0244
feature list: operation_0248
feature list: operation_0269
feature list: operation 2476
feature list: operation 3925

ALLPATHS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
citation: gr.7337908
citation: pmcid:PMC2336810
citation: pubmed:18340039
description: De novo assembly of whole-genome shotgun microreads.
feature list: operation_0310
feature list: operation_0524
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Contact Form

Allpaths-LG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0196
application sub category: topic_0199
citation: pnas.1017351108
citation: pmcid:PMC3029755
citation: pubmed:21187386
description: Short read assembler that works on both small and large (mammalian size) genomes.
feature list: operation_0310
feature list: operation 3197
license: MIT
operating system: Linux
software help: AllPaths-LG Manual.pdf
software help: computational-research-and-development
primary contact: David B. Jaffe

ALLSorts
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic 3170
application sub category: topic 3418
citation: https://doi.org/10.1101/2021.08.01.454393
description: RNA-Seq classifier for B-Cell Acute Lymphoblastic Leukemia.
feature list: operation_0314
feature list: operation 3225
feature list: operation 3436
is accessible for free: true
license: MIT
software help: 1.-Installation

almondcv2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic 3810
author: Jorge Mas Gómez
citation: https://doi.org/10.1101/2025.05.05.652179
description: Open RGB Imaging Workflow for Morphological and Morphometric Analysis
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: almondcv2

ALMOST
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 1317
application sub category: topic 2275
application sub category: topic 2814
citation: jcc.23588
citation: pubmed:24676684
description: This modelling environment provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.
feature list: operation_0477
operating system: Linux

AlmostSignificant
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3168
application sub category: topic 3393
application sub category: topic 3572
citation: BTW559
citation: pmcid:PMC5167069
citation: pubmed:27559158
description: Simplifying quality control of high-throughput sequencing data.
feature list: operation 3218
operating system: Linux
operating system: Mac
software help: AlmostSignificant
primary contact: Joe Ward

Aln2tbl
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0084
application sub category: topic_0102
application sub category: topic_0196
application sub category: topic_0621
application sub category: topic 3512
citation: https://doi.org/10.1080/23802359.2021.1966334
citation: pmcid:PMC8386716
citation: pubmed:34447886
description: Aln2tbl is a Python script for building a mitochondrial features table from a assembly alignment in fasta format. The sequencing, annotation and analysis of complete mitochondrial genomes is an important research tool in phylogeny and evolution. Starting with the primary sequence, genes features are generally annotated automatically to obtain preliminary annotations in the form of a feature table. Further manual curation in a graphic alignment editor is nevertheless necessary to revise annotations. As such, the automatically generated feature table is invalidated and has to be modified manually before submission to data banks.
feature list: operation_0310
feature list: operation_0361
feature list: operation 3431
license: GPL-3.0
primary contact: https://orcid.org/0000-0002-4683-8840

AlnC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0659
application sub category: topic_0780
application sub category: topic 3308
application sub category: topic 3512
citation: https://doi.org/10.1101/2021.02.04.429715
description: AlnC is an extensive database of long non-coding RNAs in Angiosperms.
feature list: operation_0278
feature list: operation_0436
feature list: operation 2421
feature list: operation 3431

alntools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0203
application sub category: topic_0622
application sub category: topic 3168
citation: https://doi.org/10.1101/2021.02.16.431379
description: alntools processes next-generation sequencing read alignments into a sparse compressed incidence matrix (aka Equivalence Classes) and stores it in a pre-defined binary format for efficient downstream analyses and storage. It enables us to compare, contrast, or combine the results of different alignment strategies.
feature list: operation_0292
feature list: operation 3198
feature list: operation 3359
license: MIT
software help: alntools

Alohomora
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0102
application sub category: topic_0199
application sub category: topic 2885
application sub category: topic 3053
application sub category: topic 3678
citation: bti264
citation: pubmed:15647291
description: Alohomora was designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array
feature list: operation_0283
feature list: operation 2429
operating system: Linux
operating system: Mac
operating system: Windows
software help: alohomora
software version: 0.33

alona
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Workflow
application sub category: topic_0203
application sub category: topic 2229
application sub category: topic 3170
application sub category: topic 3512
application sub category: topic 3518
citation: BTAA269
citation: pmcid:PMC7320629
citation: pubmed:32324845
description: alona is a web-based bioinformatics service designed to analyze single cell RNA sequencing (scRNA-seq) data. It is an analysis framework for single cell RNA sequencing data (scRNA-seq) and enables exploratory analysis through a set of Python modules. adobo can be used to create analysis pipelines, facilitating analysis and interpetation of scRNA-seq data.
feature list: operation_0313
feature list: operation_0571
feature list: operation 3680
feature list: operation 3933
feature list: operation 3935

ALP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0097
application sub category: topic_0622
application sub category: topic 2269
citation: btv575
citation: pmcid:PMC4739181
citation: pubmed:26428291
description: This program calculates the statistical parameters in the modified Gumbel distribution for BLAST
feature list: operation 2238
operating system: Linux
operating system: Windows
software help: alp lib v1 93.html

AlPaCas
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0199
application sub category: topic_0769
application sub category: topic_0821
application sub category: topic 3168
application sub category: topic 3912
citation: GKAE419
citation: pmcid:PMC11223865
citation: pubmed:38795068
description: AlPaCas is a web server pipeline designed to identify and analyze SNV-derived PAMs for allele-specific CRISPR gene editing. It assists in selecting Cas enzymes and proposing mutations to enhance selectivity towards SNV-derived PAMs.
feature list: operation_0272
feature list: operation 2421
feature list: operation 3227

ALPHA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0622
application sub category: topic 3293
application sub category: topic 3299
citation: bty173
citation: pubmed:29562324
description: Automated Local PHylogenomic Analyses.
feature list: operation_0324
operating system: Mac
operating system: Windows
software help: ALPHA
primary contact: Luay Nakhleh
primary contact: R A Leo Elworth

Alpha-Frag
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3474
application sub category: topic 3520
citation: https://doi.org/10.1101/2021.04.07.438629
description: Alpha-Frag is a deep neural network for fragment presence prediction improves peptide identification by data independent acquisition mass spectrometry.
feature list: operation 3631
feature list: operation 3767
feature list: operation 3799
feature list: operation 3860
license: MIT

Alpha-Tri
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3474
application sub category: topic 3520
citation: BTAB878
citation: pubmed:34999750
description: A deep neural network for scoring the similarity between predicted and measured spectra improves peptide identification of DIA data.
feature list: operation 3629
feature list: operation 3631
feature list: operation 3860
is accessible for free: true
license: Not licensed
operating system: Windows

Alpha-XIC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic 3474
application sub category: topic 3520
citation: https://doi.org/10.1101/2021.04.20.440630
description: Alpha-XIC is a deep neural network for scoring the coelution of peak groups improves peptide identification by data-independent acquisition mass spectrometry.
feature list: operation 3215
feature list: operation 3631
feature list: operation 3767

Alphabet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0154
application sub category: topic_0160
citation: pubmed:8877523
description: Alphabet takes a database of aligned protein sequences in BLOCKS+ format and examines the alignments column-wise looking for groups of amino acids that co-occur in columns more frequently than expected based on overall amino acid composition. These groups of amino acids can form a reduced alphabet for building sequence motifs (eMOTIFs) or for detecting correlations between columns of amino acids (MCSeq).
feature list: operation 2479
operating system: Linux

AlphaCharges
type: SoftwareApplication
input: UniProt ID
  type: FormalParameter
  additional type: data 2291
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Web application
application sub category: topic_0082
application sub category: topic_0154
application sub category: topic_0166
application sub category: topic 2258
description: AlphaCharges is a web server for the calculation of partial atomic charges on protein structures, created by AlphaFold.
feature list: operation_0474
feature list: operation 3431
feature list: operation 3893
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows
software help: wiki

alphaDIA
type: SoftwareApplication
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3873
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3710
  encoding format: format 3712
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0121
description: Empirical and predicted library search for label-free quantification and DIA multiplexing
feature list: operation 3631
feature list: operation 3634
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.6.2

AlphaDrop beta
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0622
application sub category: topic 2885
application sub category: topic 3053
citation: g3.111.001297
citation: pmcid:PMC3337470
citation: pubmed:22540033
description: Package for simulating genomic selection or GWAS data, that drops simulated haplotypes through a pedigree using MaCS. It can simulate sequence and SNP data, pedigrees, QTL effects, and breeding values. Pre-specified pedigrees can also be supplied.
feature list: operation 2476
operating system: Linux
operating system: Windows
software help: alphadrop
primary contact: John Hickey

AlphaESM hFolds
type: SoftwareApplication
input: UniProt accession
  type: FormalParameter
  additional type: data 3021
  encoding format: format 2330
output: Protein structure report
  type: FormalParameter
  additional type: data 1537
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic 2814
citation: j.jmb.2024.168593
citation: pubmed:38718922
description: A database for the comparison of structural models predicted by ESMFold and AlphaFold2 for human proteins.
feature list: operation 2483
is accessible for free: true
license: CC-BY-NC-4.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: help
software version: 1.0

AlphaFill
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Database portal
additional type: Script
application sub category: topic_0082
application sub category: topic_0154
application sub category: topic_0166
application sub category: topic 3047
application sub category: topic 3421
citation: s41592-022-01685-y
citation: pmcid:PMC9911346
citation: pubmed:36424442
description: AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
feature list: operation_0321
feature list: operation_0477
feature list: operation 2950
feature list: operation 3081
is accessible for free: true
license: BSD-2-Clause

AlphaFind
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web service
citation: gkae397
citation: pmcid:PMC11223785
citation: pubmed:38747341
description: AlphaFind is a web-based search engine that allows for structure-based search of the entire AlphaFold Protein Structure Database. Uniprot ID, PDB ID, or Gene Symbol is accepted as input – the engine will return the most similar proteins found within AlphaFold DB, with an option for additional search to extend and refine the results. The search results are grouped by their source organism and displayed along with several similarity metrics. 3D visualizations of the structural superposition of the proteins are provided, and text filters can be used to find specific organisms or Uniprot IDs. For details about the methodology and usage, please see the manual. This website is free and open to all users and there is no login requirement.
is accessible for free: true
software help: Manual
software version: 1.0

AlphaFold
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0082
application sub category: topic_0154
application sub category: topic_0623
application sub category: topic 2814
application sub category: topic 3474
citation: https://doi.org/10.1101/2024.02.06.579080
citation: MOLECULES29040832
citation: pmcid:PMC10893003
citation: pubmed:38398585
description: AlphaFold is an AI system developed by Google DeepMind that predicts protein 3D structures from amino acid sequences, achieving accuracy comparable to experimental methods. It is accessible through the European Bioinformatics Institute (EBI) and a GitHub repository.
feature list: operation_0303
feature list: operation_0331
feature list: operation_0474
feature list: operation 2441
feature list: operation 2487

AlphaFold2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0154
application sub category: topic 2275
application sub category: topic 2828
application sub category: topic 3336
application sub category: topic 4017
citation: ACS.JCIM.4C01388
citation: https://doi.org/10.1101/2024.09.06.611604
citation: IJMS251810139
citation: pmcid:PMC11423400
citation: pmcid:PMC11432040
citation: pubmed:39227031
citation: pubmed:39337622
description: AlphaFold2 is an AI system developed by Google DeepMind that predicts protein structures from amino acid sequences with high accuracy. It offers a web interface, API documentation, and Docker containers for users to access and utilize its capabilities in various research areas, particularly drug discovery and structural biology.
feature list: operation_0269
feature list: operation_0474
feature list: operation 2476
feature list: operation 3899
feature list: operation 3938

AlphaFold 2
type: SoftwareApplication
input: Protein sequence
  type: FormalParameter
  additional type: data 2976
  encoding format: format 1964
  encoding format: format 2200
output: Protein structure
  type: FormalParameter
  additional type: data 1460
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0130
citation: s41586-021-03819-2
citation: pmcid:PMC8371605
citation: pubmed:34265844
description: AI-guided 3D structure prediction of novel proteins. AlphaFold uses neural networks to predict the tertiary (3D) structure of proteins. AlphaFold accepts an amino acid sequence as an input, which it will then will 'fold' into a 3D model.
feature list: operation_0479
feature list: operation_0480
feature list: operation_0481
feature list: operation 2415
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: alphafold
software version: 2.0.1
software version: 2.1.0
software version: 2.1.1
software version: 2.1.2

AlphaImpute
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3056
citation: https://doi.org/10.1186/1297-9686-44-9
citation: pmcid:PMC3378429
citation: pubmed:22462519
description: Impute and phase genotype data in populations with pedigree information available. The program uses segregation analysis and haplotype library imputation to impute alleles and genotypes.
feature list: operation 3557
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows
software help: alphaimpute

AlphaKnot
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
additional type: Web application
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0736
application sub category: topic 3474
citation: gkac388
citation: pmcid:PMC9252816
citation: pubmed:35609987
description: AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values.
feature list: operation_0278
feature list: operation_0303
feature list: operation_0477
feature list: operation_0570
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows
software help: api
software help: help browse search
software help: tutorial analysis

AlphaMALIG
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
description: AlphaMALIG (ALPHAbet Multiple ALIGnment) is a tool which allows you to align many but no more than 200 sequences. These sequences will be formed by characters of a finite alphabet.
feature list: operation_0492
operating system: Linux
software version: 1.1

AlphaMap
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0601
application sub category: topic 3520
citation: https://doi.org/10.1101/2021.07.30.454433
description: An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
feature list: operation_0337
feature list: operation_0417
feature list: operation 3755
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows

Alphamod
type: SoftwareApplication
input: PDB ID
  type: FormalParameter
  additional type: data 1127
  encoding format: format 1476
  encoding format: format 1477
output: PDB ID
  type: FormalParameter
  additional type: data 1127
  encoding format: format 1476
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0091
application sub category: topic 2275
application sub category: topic 3474
citation: j.csbj.2023.10.056
citation: pmcid:PMC10690423
citation: pubmed:38047234
description: Alphamod is a novel pipeline that incorporates AlphaFold2 with MODELLER, a template-based modeling program. Additionally, our tool can drive a comprehensive quality assessment of the tertiary protein structure by incorporating and comparing a set of different quality assessment tools.
feature list: operation_0321
feature list: operation_0322
feature list: operation_0474
feature list: operation_0477
is accessible for free: true
license: Freeware
operating system: Linux
provider: ELIXIR-ITA-SALERNO
software help: Supplementary File 2.pdf

AlphaMPSim
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3053
application sub category: topic 3307
application sub category: topic 3796
citation: btu206
citation: pubmed:24872425
description: Simple software package for simulating data in multi-parent populations.
feature list: operation 2426
operating system: Linux
operating system: Mac
software help: alphampsim
primary contact: John Hickey

AlphaPart
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 3053
citation: https://doi.org/10.1101/2020.04.24.059071
description: R implementation of the method for partitioning genetic trends. Partition/Decomposition of Breeding Values by Paths of Information.
feature list: operation_0337
feature list: operation 1812
license: GPL-2.0

AlphaPept
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic_0080
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic 3520
citation: https://doi.org/10.1101/2021.07.23.453379
description: Framework for MS-based proteomics.
feature list: operation 3630
feature list: operation 3631
feature list: operation 3767
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows

AlphaPeptDeep
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0121
application sub category: topic_0154
application sub category: topic_0601
application sub category: topic 3474
application sub category: topic 3520
citation: s41467-022-34904-3
citation: pmcid:PMC9700817
citation: pubmed:36433986
description: A modular deep learning framework to predict peptide properties for proteomics.
feature list: operation_0417
feature list: operation 3629
feature list: operation 3631
feature list: operation 3633
is accessible for free: true
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows

AlphaPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0082
application sub category: topic_0121
citation: prot.10569
citation: pubmed:14997542
description: This server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.
feature list: operation_0267
feature list: operation_0492
operating system: Linux
operating system: Mac
operating system: Windows
software help: help.html
primary contact: Dr. G.P.S. Raghava

AlphaPulldown
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0128
application sub category: topic 3047
application sub category: topic 3957
citation: btac749
citation: pmcid:PMC9805587
citation: pubmed:36413069
description: A Python package for protein-protein interaction screens using AlphaFold-Multimer.
feature list: operation_0474
feature list: operation 2464
feature list: operation 2492
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

AlphaSimR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
additional type: Web application
application sub category: topic_0780
application sub category: topic 3500
application sub category: topic 3810
citation: https://doi.org/10.1101/2020.08.10.245167
description: AlphaSimR is the successor to the AlphaSim software for breeding program simulation and a package for the R software environment.
feature list: operation 2426
feature list: operation 3196
license: MIT
software help: alphasimr examples

AlphaSpace2
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0102
application sub category: topic_0128
application sub category: topic_0154
application sub category: topic_0166
application sub category: topic 2275
citation: ACS.JCIM.9B00652
citation: pmcid:PMC7093224
citation: pubmed:31995373
description: AlphaSpace2 is a surface topographical mapping tool.
feature list: operation 2429
feature list: operation 2464
feature list: operation 2492
software help: AlphaSpace2 Tutorials

AlphaTims
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0121
application sub category: topic_0769
application sub category: topic 3520
citation: J.MCPRO.2021.100149
citation: pmcid:PMC8526765
citation: pubmed:34543758
description: Indexing Trapped Ion Mobility Spectrometry-TOF Data for Fast and Easy Accession and Visualization. High-resolution MS-based proteomics generates large amounts of data, even in the standard LC-tandem MS configuration. Adding an ion mobility dimension vastly increases the acquired data volume, challenging both analytical processing pipelines and especially data exploration by scientists. This has necessitated data aggregation, effectively discarding much of the information present in these rich datasets. Taking trapped ion mobility spectrometry (TIMS) on a quadrupole TOF (Q-TOF) platform as an example, we developed an efficient indexing scheme that represents all data points as detector arrival times on scales of minutes (LC), milliseconds (TIMS), and microseconds (TOF). In our open-source AlphaTims package, data are indexed, accessed, and visualized by a combination of tools of the scientific Python ecosystem
feature list: operation_0337
feature list: operation 3435
feature list: operation 3436
license: Apache-2.0

AlphaTracker
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0769
application sub category: topic 3304
application sub category: topic 3500
citation: https://doi.org/10.1101/2020.12.04.405159
description: AlphaTracker is a multi-animal tracking and behavioral analysis tool which incorporates multi-animal tracking, pose estimation and unsupervised behavioral clustering to empower system neuroscience research. Alphatracker achieves the state-of-art accuracy of multi-animal tracking which lays the foundation for stringent biological studies. Moreover, the minimum requirement for hardware (regular webcams) and efficient training procedure allows readily adoption by most neuroscience labs.
feature list: operation 2938
feature list: operation 3432

AlphScore
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0154
application sub category: topic_0199
application sub category: topic_0769
application sub category: topic 3474
application sub category: topic 3577
citation: BTAD280
citation: pmcid:PMC10203375
citation: pubmed:37084271
description: Predicting the pathogenicity of missense variants using features derived from AlphaFold2.
feature list: operation_0331
feature list: operation 3431
feature list: operation 3461
is accessible for free: true
license: GPL-3.0
operating system: Linux
operating system: Mac
operating system: Windows

alpine
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic 2259
application sub category: topic 3170
application sub category: topic 3308
citation: nbt.3682
citation: pmcid:PMC5143225
citation: pubmed:27669167
description: Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.
feature list: operation 2426
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: alpine.html
software version: 1.0.0
primary contact: http://orcid.org/0000-0001-8401-0545

AlpsNMR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0593
application sub category: topic_0769
application sub category: topic 3172
application sub category: topic 3407
citation: BTAA022
citation: pubmed:31930381
description: AlpsNMR is an R package that can load Bruker and JDX samples as well as preprocess them.
feature list: operation 3215
feature list: operation 3435
feature list: operation 3803
license: MIT
software version: 3.1.4

ALRA
type: SoftwareApplication
input: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3475
output: Gene expression matrix
  type: FormalParameter
  additional type: data 3112
  encoding format: format 3475
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0203
application sub category: topic 3308
citation: https://doi.org/10.1101/397588
description: A method for imputation of missing values in single cell RNA-sequencing data
feature list: operation 3557
is accessible for free: true
license: Freeware
operating system: Linux
operating system: Mac
operating system: Windows
software help: ALRA
primary contact: Yuval Kluger

alsace
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic 2258
description: Alternating Least Squares (or Multivariate Curve Resolution) for analytical chemical data, in particular hyphenated data where the first direction is a retention time axis, and the second a spectral axis. Package builds on the basic als function from the ALS package and adds functionality for high-throughput analysis, including definition of time windows, clustering of profiles, retention time correction, etcetera.
feature list: operation 3432
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: alsace.pdf
software version: 1.16.0
primary contact: Ron Wehrens

Releasing synthetic data from the Avon Longitudinal Study of Parents and Children (ALSPAC)
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0625
application sub category: topic 3277
application sub category: topic 3517
application sub category: topic 4010
application sub category: topic 4045
citation: WELLCOMEOPENRES.20530.2
citation: pmcid:PMC11809151
citation: pubmed:39931104
description: This resource describes a method for generating and releasing synthetic datasets based on the Avon Longitudinal Study of Parents and Children (ALSPAC) data to facilitate transparent and reproducible research while preserving participant anonymity. The approach uses the 'synthpop' package in R and provides guidelines for researchers to follow.
feature list: operation 3283
feature list: operation 3557
feature list: operation 3659
feature list: operation 4042
software help: ALSPAC Access Policy.pdf

Alta-Cyclic
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic_0080
citation: nmeth.1230
citation: pmcid:PMC2978646
citation: pubmed:18604217
description: Alta-Cyclic is a Illumina Genome-Analyzer (Solexa) base caller.
feature list: operation 3185
operating system: Linux
software help: usage.html
primary contact: Yaniv Erlich

AltaiR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0622
application sub category: topic 3303
application sub category: topic 3307
application sub category: topic 3308
contributor: http://orcid.org/0000-0002-6331-6091
contributor: 0000-0003-1176-552X
description: AltaiR is a C toolkit for alignment-free and spatial-temporal analysis of multi-FASTA data. This method provides alignment-free and spatial-temporal analysis of multi-FASTA data through the implementation of a C toolkit that is highly flexible and with characteristics covering large-scale data, namely extensive collections of genomes/proteomes. This toolkit is ideal for scenarios entangling the presence of multiple sequences from epidemic and pandemic events. AlcoR is implemented in C language using multi-threading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence(s) in (multi-) FASTA format.
feature list: operation 2403
funder: 0000-0003-1176-552X
is accessible for free: true
license: GPL-3.0
operating system: Linux
software version: 1.0.1

AltAnalyze
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0659
application sub category: topic 3320
application sub category: topic 3512
citation: gkq405
citation: pmcid:PMC2896198
citation: pubmed:20513647
description: AltAnalyze is a comprehensive tool for the analysis of gene expression and alternative splicing data from RNA-seq and Affymetrix (exon, gene, junction) datasets at the level of proteins, domains, microRNA binding sites and pathways. The Cytoscape plugin DomainGraph (www.domaingraph.de) allows for visualization of AltAnalyze results at multiple levels of abstraction (e.g., isoform, exon, protein, domain, molecular interactions).
feature list: operation_0276
feature list: operation_0303
feature list: operation 2495
feature list: operation 2499
feature list: operation 3223
operating system: Mac
operating system: Windows
software help: latest
software help: Tutorials
primary contact: Support

altcdfenvs
type: SoftwareApplication
input: Sequence record
  type: FormalParameter
  additional type: data_0849
  encoding format: format 1929
output: Map
  type: FormalParameter
  additional type: data 1274
  encoding format: format 2060
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Library
application sub category: topic_0102
application sub category: topic_0203
citation: https://doi.org/10.1186/1471-2105-5-111
citation: pmcid:PMC514699
citation: pubmed:15310390
description: Convenience data structures and functions to handle cdfenvs.
feature list: operation_0527
license: GPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: altcdfenvs.html
software version: 2.36.0
primary contact: Laurent Gautier

ALTER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0078
application sub category: topic_0080
application sub category: topic_0654
citation: gkq321
citation: pmcid:PMC2896128
citation: pubmed:20439312
description: ALTER is a program-oriented web tool for the conversion between DNA and protein alignments.
feature list: operation_0260
feature list: operation 2479
operating system: Linux
operating system: Mac
operating system: Windows
software help: ALTER-UserGuide.htm
primary contact: ALTER Support

Altered Pathway Analyzer
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0203
application sub category: topic_0204
application sub category: topic_0602
citation: srep40450
citation: pmcid:PMC5233954
citation: pubmed:28084397
description: Cross-platform and standalone tool for analyzing gene expression datasets to highlight significantly rewired pathways across case-vs-control conditions. The Tool is designed to analyze human gene expression datasets (with Entrez ID).
feature list: operation 2497
operating system: Linux
operating system: Mac
operating system: Windows
software help: APA
software version: 3.0
primary contact: Abhinav Kaushik
primary contact: Dinesh Gupta

Alternative Splicing Gallery
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0102
application sub category: topic_0203
application sub category: topic 3120
application sub category: topic 3320
application sub category: topic 3512
citation: gkh731
citation: pmcid:PMC506815
citation: pubmed:15292448
description: The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one or more exons and download the resulting sequence. ASG also links out to other alternative splicing databases like ProSplicer.
feature list: operation_0232
feature list: operation_0264
feature list: operation_0433
feature list: operation_0526
feature list: operation 2499
operating system: Linux
operating system: Mac
operating system: Windows
primary contact: Jeremy Leipzig
primary contact: Steffen Heber

AltHapAlignR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0080
application sub category: topic_0749
application sub category: topic 3170
citation: bty125
citation: pmcid:PMC6041798
citation: pubmed:29514179
description: Method incorporating alternate reference haplotypes to generate gene- and haplotype-level estimates of transcript abundance for any genomic region where such information is available.
feature list: operation_0487
feature list: operation 3680
operating system: Linux
operating system: Mac
operating system: Windows
software help: AltHapAlignR
primary contact: Julian C Knight
primary contact: Peter Humburg

altMOD
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic 2269
application sub category: topic 2275
application sub category: topic 2814
application sub category: topic 2828
application sub category: topic 3474
citation: JOURNAL.PCBI.1007219
citation: pmcid:PMC6938380
citation: pubmed:31846452
description: Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling. altMOD is a MODELLER (https://salilab.org/modeller/) [1] plugin for improved 3D homology model building. Right now, it allows to incorporate in the program's objective function terms for interatomic distances statistical potentials, such as DOPE [2] and DFIRE [3]. The effect of adding statistical potentials in the objective function of MODELLER is described in Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling" (Janson et al., 2019). In a benchmark with 225 single-template homology models, we found that the inclusion of DOPE in the objective function of MODELLER brings an average improvement of 1.3% and 2.0% in GDT-HA [4] and lDDT [5] and a large improvement of -29.8% in MolProbity scores [6]
feature list: operation_0321
feature list: operation_0477
feature list: operation 3454

Altools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0080
application sub category: topic 2885
application sub category: topic 3517
citation: s13062-016-0110-0
citation: pmcid:PMC4756442
citation: pubmed:26883204
description: Altools is a software package that allows the precise detection of polymorphisms and structural variations.
feature list: operation 2403
license: GPL-3.0
operating system: Linux
software help: altools
primary contact: http://orcid.org/0000-0002-8874-9993

AltWOA
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic_0203
application sub category: topic 2640
application sub category: topic 3360
application sub category: topic 3500
application sub category: topic 3518
citation: J.COMPBIOMED.2022.105349
citation: pubmed:35303580
description: AltWOA is a novel feature selection algorithm where Altruistic property of candidate whales are embedded to the Whale Optimization Algorithm (WOA).
feature list: operation_0314
feature list: operation 3936
is accessible for free: true
license: MIT
operating system: Windows

Alvascience
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Suite
application sub category: topic_0154
application sub category: topic_0219
application sub category: topic_0769
application sub category: topic 3047
application sub category: topic 3474
citation: IJMS232112882
citation: pmcid:PMC9655980
citation: pubmed:36361669
description: Alvascience: A New Software Suite for the QSAR Workflow Applied to the Blood-Brain Barrier Permeability
feature list: operation 2428
feature list: operation 3799
feature list: operation 4009
is accessible for free: false
license: Proprietary
operating system: Linux
operating system: Mac
operating system: Windows

Alveolus Analysis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0634
application sub category: topic 3382
application sub category: topic 3500
citation: s12890-022-02274-7
citation: pmcid:PMC9759058
citation: pubmed:36528564
description: A web browser-based tool to analyze lung intravital microscopy.
feature list: operation_0337
feature list: operation 3443
feature list: operation 3937
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

Alview
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0092
application sub category: topic_0622
application sub category: topic 2640
application sub category: topic 3307
citation: cin.s26470
citation: pmcid:PMC4573065
citation: pubmed:26417198
description: Fast bam file viewer from the National Cancer Informatics Program.
feature list: operation 3208
operating system: Linux
operating system: Mac
operating system: Windows
software help: alview
primary contact: Richard P. Finney

Alvin
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
additional type: Web application
application sub category: topic 2259
application sub category: topic 3300
application sub category: topic 3315
citation: https://doi.org/10.1101/2021.09.15.460416
description: Interactive, visual simulation of a spatio-temporal model of gas exchange in the human alveolus. In interdisciplinary fields such as systems biology, close collaboration between experimentalists and theorists is crucial for the success of a project. Theoretical modeling in physiology usually describes complex systems with many interdependencies. On one hand, these models have to be grounded on experimental data. On the other hand, experimenters must be able to penetrate the model in its dependencies in order to correctly interpret the results in the physiological context. When theorists and experimenters collaborate, communicating results and ideas is sometimes challenging. We promote interactive, visual simulations as an engaging way to communicate theoretical models in physiology and to thereby advance our understanding of the process of interest
feature list: operation_0337
feature list: operation 2426
feature list: operation 3435

Alvis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0080
application sub category: topic_0622
application sub category: topic 3382
citation: S12859-021-04056-0
citation: pmcid:PMC7967992
citation: pubmed:33726674
description: Alvis is a tool for contig and read ALignment VISualisation and chimera detection. It produces LaTeX and SVG alignment diagrams from a number of common alignment formats.
feature list: operation_0292
feature list: operation_0337
feature list: operation_0450
feature list: operation 1812
feature list: operation 3198
software help: latest
primary contact: https://orcid.org/0000-0003-3044-4297

Selective Neuronal Vulnerability Alzheimer Disease
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0634
application sub category: topic 3304
application sub category: topic 3474
citation: J.NEURON.2020.06.010
citation: pmcid:PMC7580783
citation: pubmed:32603655
description: Selective Neuronal Vulnerability in Alzheimer's Disease.
feature list: operation 2436
feature list: operation 3450
feature list: operation 3799

Alz-disc
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0199
application sub category: topic_0634
application sub category: topic 3474
citation: https://doi.org/10.2174/1386207325666220520102316
citation: pubmed:35619290
description: A tool to discriminate disease-causing and neutral mutations in Alzheimer's disease.
feature list: operation 4009
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

AlzCode
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Workflow
application sub category: topic_0203
application sub category: topic_0602
application sub category: topic_0625
application sub category: topic_0634
application sub category: topic 3170
citation: BTAC033
citation: pubmed:35040932
description: AlzCode is a web resource that developed pipeline to evaluate the association of genes with AD. The association of genes with AD are validated by multiple lines of functional genomic evidence with statistical approaches.
feature list: operation 1781
feature list: operation 3223
feature list: operation 3463
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

AlzGPS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0121
application sub category: topic_0202
application sub category: topic_0602
application sub category: topic 3375
application sub category: topic 3379
citation: https://doi.org/10.1101/2020.09.17.302612
description: A Genome-wide Positioning Systems Platform to Catalyze Multi-omics for Alzheimer’s Therapeutic Discovery. A Network-based multi-omics analysis informs Alzheimer's patient care and therapeutic development.
feature list: operation 2421
feature list: operation 3431
feature list: operation 3925

AlzScPred
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
citation: https://doi.org/10.1101/2023.07.07.548171
description: AlzScPred - A Package to Predict Alzheimer's Disease Using Single Cell Data

AM-UNet
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workbench
application sub category: topic 3304
application sub category: topic 3384
application sub category: topic 3444
citation: S11042-021-11568-7
citation: pmcid:PMC8742670
citation: pubmed:35035265
description: AM-UNet: Automated Mini 3D End-to-End U-NetBased Network For Brain Claustrum Segmentation.
feature list: operation 3927
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

Amadis
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0219
application sub category: topic_0634
application sub category: topic 3407
application sub category: topic 3941
citation: FPHYS.2021.697059
citation: pmcid:PMC8317061
citation: pubmed:34335304
description: A Comprehensive Database for Association Between Microbiota and Disease.
feature list: operation 2421
feature list: operation 3925
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

AMALPHI
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0611
application sub category: topic 2828
application sub category: topic 3373
application sub category: topic 3474
citation: acs.molpharmaceut.3c00964
citation: pmcid:PMC10853961
citation: pubmed:38134445
description: A machine learning platform for predicting drug-induced phosphol ipidosis.
feature list: operation 2428
feature list: operation 3891
feature list: operation 3938
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

Amanida
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic 3172
application sub category: topic 3379
citation: btab591
citation: pmcid:PMC8722753
citation: pubmed:34406360
description: An R package for Meta-analysis of metabolomics non-integral data.
feature list: operation_0337
feature list: operation 3435
feature list: operation 3799
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

AMAS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
additional type: Plug-in
application sub category: topic_0080
application sub category: topic_0194
application sub category: topic 2269
application sub category: topic 3293
citation: peerj.1660
citation: pmcid:PMC4734057
citation: pubmed:26835189
description: AMAS (Alignment Manipulation And Summary), a tool that works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics.
feature list: operation 2478
feature list: operation 2479
license: GPL-3.0
operating system: Linux
operating system: Windows
software help: README.md
primary contact: Marek L. Borowiec

AMASS
type: SoftwareApplication
input: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3464
  encoding format: format 3579
  encoding format: format 3591
  encoding format: format 3603
  encoding format: format 3752
input: Mass spectrometry data
  type: FormalParameter
  additional type: data 2536
  encoding format: format 3245
output: Report
  type: FormalParameter
  additional type: data 2048
  encoding format: format 3508
  encoding format: format 3752
output: Image
  type: FormalParameter
  additional type: data 2968
  encoding format: format 3464
  encoding format: format 3579
  encoding format: format 3591
  encoding format: format 3603
  encoding format: format 3752
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic 3382
application sub category: topic 3520
citation: pr2005378
citation: pmcid:PMC3190602
citation: pubmed:21800894
description: Series of tools written in C++ that allows you to segment your mass spectrometry imaging dataset into regions with similar molecular signatures. The software allows for user input at each step of the process and returns the regions as well as the associated molecular signatures. It is composed of two dynamic libraries and a series of executables using the libraries as a base.
feature list: operation 3214
feature list: operation 3443
operating system: Linux
operating system: Windows
software help: usage

AMASS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
application sub category: topic 3301
application sub category: topic 3305
application sub category: topic 3324
application sub category: topic 3337
application sub category: topic 3575
citation: https://doi.org/10.1101/2020.04.27.20072025
description: Automated tool for antimicrobial resistance surveillance system (AMASS) was developed as an offline, open-access and easy-to-use application that allows a hospital to perform data analysis independently and generate isolate-based and sample-based surveillance reports stratified by infection origin from routinely collected electronic databases. The application was built in R, which is a free software environment.
feature list: operation 3431

AMAT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Script
additional type: Workbench
application sub category: topic 3063
application sub category: topic 3315
application sub category: topic 3697
citation: LQAB120
citation: pmcid:PMC8759573
citation: pubmed:35047812
description: Adaptive and powerful microbiome multivariate association analysis via feature selection.
feature list: operation_0324
feature list: operation 3435
feature list: operation 3936
is accessible for free: true
license: Not licensed
operating system: Linux
operating system: Mac
operating system: Windows

aMatReader
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic 3315
citation: f1000research.15146.1
description: Augments the Cytoscape network readers by adding the ability to read in an adjacency matrix.
feature list: operation 2409
operating system: Linux
operating system: Mac
operating system: Windows
software version: 1.1.3

AmazonForest
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0154
application sub category: topic_0625
application sub category: topic 2269
application sub category: topic 3676
citation: PREPRINTS202011.0519.V1
description: A web tool to query data for a set of 5k variants that were predicted with high pathogenic probability
feature list: operation_0307
feature list: operation 3225
feature list: operation 3461

AMBAR
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0154
application sub category: topic_0199
application sub category: topic 2640
application sub category: topic 3168
application sub category: topic 3577
citation: V1
description: An R-package for interactive alteration annotations for molecular tumor boards.
feature list: operation_0337
feature list: operation 3227
feature list: operation 3695

AMBER
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 2275
application sub category: topic 3307
citation: jcc.20290
citation: wcms.1121
citation: pmcid:PMC1989667
citation: pubmed:16200636
description: The Assisted Model Building with Energy Refinement tool refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
feature list: operation 2426
operating system: Linux
operating system: Mac
operating system: Windows
software help: doc12

AmberGPUMDSimulation
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Plug-in
application sub category: topic_0176
citation: j.bpj.2017.04.055
citation: pmcid:PMC5479118
citation: pubmed:28636905
description: An automated workflow tool for Kepler to perform AMBER GPU molecular dynamics simulations.
feature list: operation 2476
license: LGPL-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: AmberGPUMDSimulation 1.1 manual.pdf
primary contact: Rommie E. Amaro

AmberMDrun
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0176
application sub category: topic_0209
application sub category: topic 2275
citation: biom13040635
citation: pmcid:PMC10135445
citation: pubmed:37189382
description: A scripting tool for running amber MD in an easy way.
feature list: operation_0482
feature list: operation 2476
feature list: operation 3893
feature list: operation 4009
is accessible for free: true
license: MIT
operating system: Linux
operating system: Mac
operating system: Windows

AmberTools
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Suite
application sub category: topic_0176
application sub category: topic 2275
citation: jcc.20290
citation: pmcid:PMC1989667
citation: pubmed:16200636
description: Consists of several independently developed packages that work well by themselves, and with Amber (Assisted Model Building with Energy Refinement) itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models.
feature list: operation 2476
operating system: Linux
operating system: Mac
operating system: Windows
software help: doc12

AMBIENT
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0602
application sub category: topic 2259
application sub category: topic 3172
citation: https://doi.org/10.1186/1752-0509-7-26
citation: pmcid:PMC3656802
citation: pubmed:23531303
description: The Active Modules for Bipartite Networks is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have some consistent characteristic. It does not require predefined pathways and gives highly specific predictions of affected areas of metabolism.
feature list: operation 3660
operating system: Linux
operating system: Mac
operating system: Windows
software help: ambient-bio
primary contact: William Bryant

Ambit-SLN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0154
application sub category: topic_0769
application sub category: topic 2258
application sub category: topic 3314
citation: MINF.202100027
citation: pubmed:34342942
description: Open Source Software Library for Processing of Chemical Objects via SLN Linear Notation.
feature list: operation 1812
feature list: operation 2421
feature list: operation 3502
is accessible for free: true
license: LGPL-3.0

Ambit-SMIRKS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
application sub category: topic_0821
application sub category: topic 2258
application sub category: topic 2814
application sub category: topic 3172
citation: s13321-018-0295-6
citation: pmcid:PMC6102164
citation: pubmed:30128804
description: Software module for reaction representation, reaction search and structure transformation.
feature list: operation 2497
license: Apache-2.0
operating system: Linux
operating system: Mac
operating system: Windows
software help: install ambitrest.html
primary contact: Support

AMBP
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Web application
additional type: Workflow
application sub category: topic_0102
application sub category: topic_0625
application sub category: topic_0769
application sub category: topic 3168
application sub category: topic 3518
citation: gkac424
citation: pmcid:PMC9252723
citation: pubmed:35639514
description: Aquaculture Molecular Breeding Platform (AMBP): a web server and standalone version for genotype imputation and genetic analysis in aquaculture
feature list: operation_0487
feature list: operation 3196
feature list: operation 3557
feature list: operation 3891
is accessible for free: true
license: Other
operating system: Linux
operating system: Mac
operating system: Windows

AMC
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Command-line tool
application sub category: topic_0199
application sub category: topic_0625
application sub category: topic 3293
citation: BTAB857
citation: pubmed:34951625
description: Accurate mutation clustering from single-cell sequencing data.
feature list: operation 3196
feature list: operation 3432
feature list: operation 3478
is accessible for free: true
license: GPL-3.0
operating system: Linux

Animal Metabolite Database
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Database portal
application sub category: topic_0154
application sub category: topic_0593
application sub category: topic 3172
application sub category: topic 3500
application sub category: topic 3520
citation: METABO13101088
citation: pmcid:PMC10609207
citation: pubmed:37887413
description: Metabolite concentrations in animal tissues and convenient comparison of quantitative metabolomic data.
feature list: operation 3431
feature list: operation 3799
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows

AMDock
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic_0209
application sub category: topic 2275
application sub category: topic 3382
citation: S13062-020-00267-2
citation: pmcid:PMC7493944
citation: pubmed:32938494
description: A versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4.
feature list: operation_0337
feature list: operation_0482
operating system: Linux
operating system: Windows

AMEBaS
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Workflow
application sub category: topic 2229
application sub category: topic 2640
application sub category: topic 3064
application sub category: topic 3382
citation: https://doi.org/10.3791/64857
citation: pubmed:37427934
description: Automatic Midline Extraction and Background Subtraction of Ratiometric Fluorescence Time-Lapses of Polarized Single Cells. AMEBaS is a new computer program that has been developed to automate the study of cells with polarity and is based in pollen tube growth and ion dynamics data. This program uses a three-step process to analyze fluorescent markers in cells with polarity.
feature list: operation 3446
feature list: operation 3799
is accessible for free: true

AMEN
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Desktop application
application sub category: topic 3391
citation: https://doi.org/10.1186/1471-2105-9-86
citation: pmcid:PMC2375118
citation: pubmed:18254954
description: The Annotation, Mapping, Expression and Network (AMEN) software is a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i) uploading and pre-processing data from microarray expression profiling experiments, (ii) detecting groups of significantly co-expressed genes, and (iii) searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human.
feature list: operation 2495
feature list: operation 3083
feature list: operation 3501
is accessible for free: true
software version: 1.5.4
primary contact: http://orcid.org/0000-0002-0535-3628

AMEND
type: SoftwareApplication
conforms to: https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT
additional type: Library
application sub category: topic_0121
application sub category: topic_0128
application sub category: topic 3170
application sub category: topic 3308
application sub category: topic 3518
citation: s12859-023-05376-z
citation: pmcid:PMC10324253
citation: pubmed:37415126
description: AMEND (Active Module identification using Experimental data and Network Diffusion) is an algorithm designed to find a subset of connected nodes in a molecular interaction network that have large experimental values. It makes use of random walk with restart (RWR) to create node weights, and a heuristic approach for solving the Maximum-weight Connected Subgraph problem using these weights. The resulting subnetwork is then scored based on average experimental values and connectivity, and it is used as input into RWR for the next iteration. This process is performed iteratively until an optimal subnetwork (i.e., module) is found.
feature list: operation 3223
feature list: operation 3501
feature list: operation 3927
is accessible for free: true
operating system: Linux
operating system: Mac
operating system: Windows